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-:3c16ed8faa07
+package Apache::Authn::SoundSoftware;
 =head1 Apache::Authn::SoundSoftware
 SoundSoftware - a mod_perl module for Apache authentication against a
 Redmine database and optional LDAP implementing the access control
 rules required for the SoundSoftware.ac.uk repository site.
 =head1 SYNOPSIS
 This module is closely based on the Redmine.pm authentication module
 provided with Redmine.  It is intended to be used for authentication
 in front of a repository service such as hgwebdir.
 Requirements:
 . Clone/pull from repo for public project: Any user, no
 authentication required
 . Clone/pull from repo for private project: Project members only
 . Push to repo for public project: "Permitted" users only (this
-:0c83d98252d9
+probably means project members who are also identified in the hgrc web
 section for the repository and so will be approved by hgwebdir?)
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+. Push to repo for private project: "Permitted" users only (as above)
-:3c16ed8faa07
+            Chris
-:034e9b00b341
+. Push to any repo that is tracking an external repo: Refused always
-:3c16ed8faa07
+=head1 INSTALLATION
 Debian/ubuntu:
   apt-get install libapache-dbi-perl libapache2-mod-perl2 \
     libdbd-mysql-perl libauthen-simple-ldap-perl libio-socket-ssl-perl
 Note that LDAP support is hardcoded "on" in this script (it is
 optional in the original Redmine.pm).
 =head1 CONFIGURATION
    ## This module has to be in your perl path
    ## eg:  /usr/local/lib/site_perl/Apache/Authn/SoundSoftware.pm
    PerlLoadModule Apache::Authn::SoundSoftware
    # Example when using hgwebdir
    ScriptAlias / "/var/hg/hgwebdir.cgi/"
    <Location />
        AuthName "Mercurial"
        AuthType Basic
        Require valid-user
        PerlAccessHandler Apache::Authn::SoundSoftware::access_handler
        PerlAuthenHandler Apache::Authn::SoundSoftware::authen_handler
        SoundSoftwareDSN "DBI:mysql:database=redmine;host=localhost"
        SoundSoftwareDbUser "redmine"
        SoundSoftwareDbPass "password"
        Options +ExecCGI
        AddHandler cgi-script .cgi
        ## Optional where clause (fulltext search would be slow and
        ## database dependant).
        # SoundSoftwareDbWhereClause "and members.role_id IN (1,2)"
-:0c83d98252d9
+       ## Optional prefix for local repository URLs
        # SoundSoftwareRepoPrefix "/var/hg/"
-:3c16ed8faa07
+  </Location>
 See the original Redmine.pm for further configuration notes.
 =cut
 use strict;
 use warnings FATAL => 'all', NONFATAL => 'redefine';
 use DBI;
 use Digest::SHA1;
 use Authen::Simple::LDAP;
 use Apache2::Module;
 use Apache2::Access;
 use Apache2::ServerRec qw();
 use Apache2::RequestRec qw();
 use Apache2::RequestUtil qw();
 use Apache2::Const qw(:common :override :cmd_how);
 use APR::Pool ();
 use APR::Table ();
 my @directives = (
+  {
     name => 'SoundSoftwareDSN',
     req_override => OR_AUTHCFG,
     args_how => TAKE1,
     errmsg => 'Dsn in format used by Perl DBI. eg: "DBI:Pg:dbname=databasename;host=my.db.server"',
   },
+  {
     name => 'SoundSoftwareDbUser',
     req_override => OR_AUTHCFG,
     args_how => TAKE1,
   },
+  {
     name => 'SoundSoftwareDbPass',
     req_override => OR_AUTHCFG,
     args_how => TAKE1,
   },
+  {
     name => 'SoundSoftwareDbWhereClause',
     req_override => OR_AUTHCFG,
     args_how => TAKE1,
   },
+  {
-:0c83d98252d9
+    name => 'SoundSoftwareRepoPrefix',
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+    req_override => OR_AUTHCFG,
     args_how => TAKE1,
   },
 );
 sub SoundSoftwareDSN {
-:0c83d98252d9
+    my ($self, $parms, $arg) = @_;
     $self->{SoundSoftwareDSN} = $arg;
     my $query = "SELECT
-:3c16ed8faa07
+                 hashed_password, auth_source_id, permissions
               FROM members, projects, users, roles, member_roles
               WHERE
                 projects.id=members.project_id
                 AND member_roles.member_id=members.id
                 AND users.id=members.user_id
                 AND roles.id=member_roles.role_id
                 AND users.status=1
                 AND login=?
                 AND identifier=? ";
-:0c83d98252d9
+    $self->{SoundSoftwareQuery} = trim($query);
-:3c16ed8faa07
+            Chris
 sub SoundSoftwareDbUser { set_val('SoundSoftwareDbUser', @_); }
 sub SoundSoftwareDbPass { set_val('SoundSoftwareDbPass', @_); }
 sub SoundSoftwareDbWhereClause {
-:0c83d98252d9
+    my ($self, $parms, $arg) = @_;
     $self->{SoundSoftwareQuery} = trim($self->{SoundSoftwareQuery}.($arg ? $arg : "")." ");
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+sub SoundSoftwareRepoPrefix {
     my ($self, $parms, $arg) = @_;
     if ($arg) {
 	$self->{SoundSoftwareRepoPrefix} = $arg;
+    }
-:3c16ed8faa07
+            Chris
 sub trim {
-:0c83d98252d9
+    my $string = shift;
     $string =~ s/\s{2,}/ /g;
     return $string;
-:3c16ed8faa07
+            Chris
 sub set_val {
-:0c83d98252d9
+    my ($key, $self, $parms, $arg) = @_;
     $self->{$key} = $arg;
-:3c16ed8faa07
+            Chris
 Apache2::Module::add(__PACKAGE__, \@directives);
 my %read_only_methods = map { $_ => 1 } qw/GET PROPFIND REPORT OPTIONS/;
 sub access_handler {
-:0c83d98252d9
+    my $r = shift;
-:3c16ed8faa07
+            Chris
-:a389c77da9fd
+    print STDERR "SoundSoftware.pm: In access handler at " . scalar localtime() . "\n";
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+    unless ($r->some_auth_required) {
 	$r->log_reason("No authentication has been configured");
 	return FORBIDDEN;
+    }
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+    my $method = $r->method;
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+    print STDERR "SoundSoftware.pm: Method: $method, uri " . $r->uri . ", location " . $r->location . "\n";
     print STDERR "SoundSoftware.pm: Accept: " . $r->headers_in->{Accept} . "\n";
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+    my $dbh = connect_database($r);
-:a389c77da9fd
+    unless ($dbh) {
 	print STDERR "SoundSoftware.pm: Database connection failed!: " . $DBI::errstr . "\n";
 	return FORBIDDEN;
+    }
-:034e9b00b341
+    print STDERR "Connected to db, dbh is " . $dbh . "\n";
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+    my $project_id = get_project_identifier($dbh, $r);
-:034e9b00b341
+            chris
     if (!defined $read_only_methods{$method}) {
         print STDERR "SoundSoftware.pm: Method is not read-only\n";
         if (project_repo_is_readonly($dbh, $project_id, $r)) {
             print STDERR "SoundSoftware.pm: Project repo is read-only, refusing access\n";
 	    return FORBIDDEN;
         } else {
 	    print STDERR "SoundSoftware.pm: Project repo is read-write, authentication handler required\n";
             return OK;
+        }
+    }
-:0c83d98252d9
+    my $status = get_project_status($dbh, $project_id, $r);
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+    $dbh->disconnect();
     undef $dbh;
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+    if ($status == 0) { # nonexistent
 	print STDERR "SoundSoftware.pm: Project does not exist, refusing access\n";
 	return FORBIDDEN;
     } elsif ($status == 1) { # public
 	print STDERR "SoundSoftware.pm: Project is public, no restriction here\n";
 	$r->set_handlers(PerlAuthenHandler => [\&OK])
     } else { # private
 	print STDERR "SoundSoftware.pm: Project is private, authentication handler required\n";
+    }
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+    return OK
-:3c16ed8faa07
+            Chris
 sub authen_handler {
-:0c83d98252d9
+    my $r = shift;
-:a389c77da9fd
+    print STDERR "SoundSoftware.pm: In authentication handler at " . scalar localtime() . "\n";
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+    my $dbh = connect_database($r);
-:a389c77da9fd
+    unless ($dbh) {
         print STDERR "SoundSoftware.pm: Database connection failed!: " . $DBI::errstr . "\n";
         return AUTH_REQUIRED;
+    }
-:0c83d98252d9
+            Chris
     my $project_id = get_project_identifier($dbh, $r);
     my $realm = get_realm($dbh, $project_id, $r);
     $r->auth_name($realm);
     my ($res, $redmine_pass) =  $r->get_basic_auth_pw();
     unless ($res == OK) {
 	$dbh->disconnect();
 	undef $dbh;
 	return $res;
+    }
     print STDERR "SoundSoftware.pm: User is " . $r->user . ", got password\n";
     my $permitted = is_permitted($dbh, $project_id, $r->user, $redmine_pass, $r);
     $dbh->disconnect();
     undef $dbh;
     if ($permitted) {
 	return OK;
     } else {
 	print STDERR "SoundSoftware.pm: Not permitted\n";
 	$r->note_auth_failure();
 	return AUTH_REQUIRED;
+    }
-:3c16ed8faa07
+            Chris
 sub get_project_status {
-:0c83d98252d9
+    my $dbh = shift;
-:3c16ed8faa07
+    my $project_id = shift;
     my $r = shift;
-:0c83d98252d9
+            Chris
     if (!defined $project_id or $project_id eq '') {
 	return 0; # nonexistent
+    }
-:3c16ed8faa07
+            Chris
     my $sth = $dbh->prepare(
         "SELECT is_public FROM projects WHERE projects.identifier = ?;"
     );
     $sth->execute($project_id);
-:0c83d98252d9
+    my $ret = 0; # nonexistent
-:3c16ed8faa07
+    if (my @row = $sth->fetchrow_array) {
     	if ($row[0] eq "1" || $row[0] eq "t") {
 	    $ret = 1; # public
     	} else {
-:0c83d98252d9
+	    $ret = 2; # private
-:3c16ed8faa07
+            Chris
+    }
     $sth->finish();
     undef $sth;
     $ret;
+}
-:034e9b00b341
+sub project_repo_is_readonly {
     my $dbh = shift;
     my $project_id = shift;
     my $r = shift;
     if (!defined $project_id or $project_id eq '') {
         return 0; # nonexistent
+    }
     my $sth = $dbh->prepare(
         "SELECT repositories.is_external FROM repositories, projects WHERE projects.identifier = ? AND repositories.project_id = projects.id;"
     );
     $sth->execute($project_id);
     my $ret = 0; # nonexistent
     if (my @row = $sth->fetchrow_array) {
-:6d3f8aeb51b7
+        if (defined($row[0]) && ($row[0] eq "1" || $row[0] eq "t")) {
-:034e9b00b341
+            $ret = 1; # read-only (i.e. external)
         } else {
             $ret = 0; # read-write
+        }
+    }
     $sth->finish();
     undef $sth;
     $ret;
+}
-:0c83d98252d9
+sub is_permitted {
     my $dbh = shift;
     my $project_id = shift;
     my $redmine_user = shift;
     my $redmine_pass = shift;
     my $r = shift;
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+    my $pass_digest = Digest::SHA1::sha1_hex($redmine_pass);
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+    my $cfg = Apache2::Module::get_config
 	(__PACKAGE__, $r->server, $r->per_dir_config);
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+    my $query = $cfg->{SoundSoftwareQuery};
     my $sth = $dbh->prepare($query);
     $sth->execute($redmine_user, $project_id);
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+    my $ret;
     while (my ($hashed_password, $auth_source_id, $permissions) = $sth->fetchrow_array) {
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+	# Test permissions for this user before we verify credentials
 	# -- if the user is not permitted this action anyway, there's
 	# not much point in e.g. contacting the LDAP
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+	my $method = $r->method;
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+	if ((defined $read_only_methods{$method} && $permissions =~ /:browse_repository/)
 	    || $permissions =~ /:commit_access/) {
 	    # User would be permitted this action, if their
 	    # credentials checked out -- test those now
 	    print STDERR "SoundSoftware.pm: User $redmine_user has required role, checking credentials\n";
 	    unless ($auth_source_id) {
 		if ($hashed_password eq $pass_digest) {
 		    print STDERR "SoundSoftware.pm: User $redmine_user authenticated via password\n";
 		    $ret = 1;
 		    last;
+		}
 	    } else {
 		my $sthldap = $dbh->prepare(
 		    "SELECT host,port,tls,account,account_password,base_dn,attr_login FROM auth_sources WHERE id = ?;"
 		    );
 		$sthldap->execute($auth_source_id);
 		while (my @rowldap = $sthldap->fetchrow_array) {
 		    my $ldap = Authen::Simple::LDAP->new(
 			host    => ($rowldap[2] eq "1" || $rowldap[2] eq "t") ? "ldaps://$rowldap[0]" : $rowldap[0],
 			port    => $rowldap[1],
 			basedn  => $rowldap[5],
 			binddn  => $rowldap[3] ? $rowldap[3] : "",
 			bindpw  => $rowldap[4] ? $rowldap[4] : "",
 			filter  => "(".$rowldap[6]."=%s)"
 			);
 		    if ($ldap->authenticate($redmine_user, $redmine_pass)) {
 			print STDERR "SoundSoftware.pm: User $redmine_user authenticated via LDAP\n";
 			$ret = 1;
+		    }
+		}
 		$sthldap->finish();
 		undef $sthldap;
+	    }
 	} else {
 	    print STDERR "SoundSoftware.pm: User $redmine_user lacks required role for this project\n";
+	}
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+    $sth->finish();
     undef $sth;
     $ret;
-:3c16ed8faa07
+            Chris
 sub get_project_identifier {
-:0c83d98252d9
+    my $dbh = shift;
-:3c16ed8faa07
+    my $r = shift;
     my $location = $r->location;
     my ($repo) = $r->uri =~ m{$location/*([^/]+)};
-:2c10dc5f122d
+            Chris
     return $repo if (!$repo);
-:3c16ed8faa07
+    $repo =~ s/[^a-zA-Z0-9\._-]//g;
-:0c83d98252d9
+    # The original Redmine.pm returns the string just calculated as
     # the project identifier.  That won't do for us -- we may have
     # (and in fact already do have, in our test instance) projects
     # whose repository names differ from the project identifiers.
     # This is a rather fundamental change because it means that almost
     # every request needs more than one database query -- which
     # prompts us to start passing around $dbh instead of connecting
     # locally within each function as is done in Redmine.pm.
-:3c16ed8faa07
+    my $sth = $dbh->prepare(
         "SELECT projects.identifier FROM projects, repositories WHERE repositories.project_id = projects.id AND repositories.url LIKE ?;"
     );
-:0c83d98252d9
+    my $cfg = Apache2::Module::get_config
 	(__PACKAGE__, $r->server, $r->per_dir_config);
     my $prefix = $cfg->{SoundSoftwareRepoPrefix};
     if (!defined $prefix) { $prefix = '%/'; }
-:3c16ed8faa07
+    my $identifier = '';
-:0c83d98252d9
+    $sth->execute($prefix . $repo);
-:3c16ed8faa07
+    my $ret = 0;
     if (my @row = $sth->fetchrow_array) {
 	$identifier = $row[0];
+    }
     $sth->finish();
     undef $sth;
-:0c83d98252d9
+    print STDERR "SoundSoftware.pm: Repository '$repo' belongs to project '$identifier'\n";
-:3c16ed8faa07
+            Chris
     $identifier;
+}
-:0c83d98252d9
+sub get_realm {
     my $dbh = shift;
     my $project_id = shift;
     my $r = shift;
     my $sth = $dbh->prepare(
         "SELECT projects.name FROM projects WHERE projects.identifier = ?;"
     );
     my $name = $project_id;
     $sth->execute($project_id);
     my $ret = 0;
     if (my @row = $sth->fetchrow_array) {
 	$name = $row[0];
+    }
     $sth->finish();
     undef $sth;
     # be timid about characters not permitted in auth realm and revert
     # to project identifier if any are found
     if ($name =~ m/[^\w\d\s\._-]/) {
 	$name = $project_id;
+    }
     my $realm = '"Mercurial repository for ' . "'$name'" . '"';
     $realm;
+}
-:3c16ed8faa07
+sub connect_database {
     my $r = shift;
-:0c83d98252d9
+    my $cfg = Apache2::Module::get_config
 	(__PACKAGE__, $r->server, $r->per_dir_config);
     return DBI->connect($cfg->{SoundSoftwareDSN},
-:a389c77da9fd
+	                $cfg->{SoundSoftwareDbUser},
 		        $cfg->{SoundSoftwareDbPass});
-:3c16ed8faa07
+            Chris
 ;
 package Apache::Authn::SoundSoftware;
 =head1 Apache::Authn::SoundSoftware
 SoundSoftware - a mod_perl module for Apache authentication against a
 Redmine database and optional LDAP implementing the access control
 rules required for the SoundSoftware.ac.uk repository site.
 =head1 SYNOPSIS
 This module is closely based on the Redmine.pm authentication module
 provided with Redmine.  It is intended to be used for authentication
 in front of a repository service such as hgwebdir.
 Requirements:
 . Clone/pull from repo for public project: Any user, no
 authentication required
 . Clone/pull from repo for private project: Project members only
 . Push to repo for public project: "Permitted" users only (this
-:0c83d98252d9
+probably means project members who are also identified in the hgrc web
 section for the repository and so will be approved by hgwebdir?)
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+. Push to repo for private project: "Permitted" users only (as above)
-:3c16ed8faa07
+            Chris
-:034e9b00b341
+. Push to any repo that is tracking an external repo: Refused always
-:3c16ed8faa07
+=head1 INSTALLATION
 Debian/ubuntu:
   apt-get install libapache-dbi-perl libapache2-mod-perl2 \
     libdbd-mysql-perl libauthen-simple-ldap-perl libio-socket-ssl-perl
 Note that LDAP support is hardcoded "on" in this script (it is
 optional in the original Redmine.pm).
 =head1 CONFIGURATION
    ## This module has to be in your perl path
    ## eg:  /usr/local/lib/site_perl/Apache/Authn/SoundSoftware.pm
    PerlLoadModule Apache::Authn::SoundSoftware
    # Example when using hgwebdir
    ScriptAlias / "/var/hg/hgwebdir.cgi/"
    <Location />
        AuthName "Mercurial"
        AuthType Basic
        Require valid-user
        PerlAccessHandler Apache::Authn::SoundSoftware::access_handler
        PerlAuthenHandler Apache::Authn::SoundSoftware::authen_handler
        SoundSoftwareDSN "DBI:mysql:database=redmine;host=localhost"
        SoundSoftwareDbUser "redmine"
        SoundSoftwareDbPass "password"
        Options +ExecCGI
        AddHandler cgi-script .cgi
        ## Optional where clause (fulltext search would be slow and
        ## database dependant).
        # SoundSoftwareDbWhereClause "and members.role_id IN (1,2)"
-:0c83d98252d9
+       ## Optional prefix for local repository URLs
        # SoundSoftwareRepoPrefix "/var/hg/"
-:3c16ed8faa07
+  </Location>
 See the original Redmine.pm for further configuration notes.
 =cut
 use strict;
 use warnings FATAL => 'all', NONFATAL => 'redefine';
 use DBI;
-:1e9b1bdd062e
+use Digest::SHA;
-:3c16ed8faa07
+use Authen::Simple::LDAP;
 use Apache2::Module;
 use Apache2::Access;
 use Apache2::ServerRec qw();
 use Apache2::RequestRec qw();
 use Apache2::RequestUtil qw();
 use Apache2::Const qw(:common :override :cmd_how);
 use APR::Pool ();
 use APR::Table ();
 my @directives = (
+  {
     name => 'SoundSoftwareDSN',
     req_override => OR_AUTHCFG,
     args_how => TAKE1,
     errmsg => 'Dsn in format used by Perl DBI. eg: "DBI:Pg:dbname=databasename;host=my.db.server"',
   },
+  {
     name => 'SoundSoftwareDbUser',
     req_override => OR_AUTHCFG,
     args_how => TAKE1,
   },
+  {
     name => 'SoundSoftwareDbPass',
     req_override => OR_AUTHCFG,
     args_how => TAKE1,
   },
+  {
     name => 'SoundSoftwareDbWhereClause',
     req_override => OR_AUTHCFG,
     args_how => TAKE1,
   },
+  {
-:0c83d98252d9
+    name => 'SoundSoftwareRepoPrefix',
-:3c16ed8faa07
+    req_override => OR_AUTHCFG,
     args_how => TAKE1,
   },
-:897bc2b63bfe
+            Chris
     name => 'SoundSoftwareSslRequired',
     req_override => OR_AUTHCFG,
     args_how => TAKE1,
   },
-:3c16ed8faa07
+);
 sub SoundSoftwareDSN {
-:0c83d98252d9
+    my ($self, $parms, $arg) = @_;
     $self->{SoundSoftwareDSN} = $arg;
     my $query = "SELECT
-:6d3f8aeb51b7
+                 hashed_password, salt, auth_source_id, permissions
-:3c16ed8faa07
+              FROM members, projects, users, roles, member_roles
               WHERE
                 projects.id=members.project_id
                 AND member_roles.member_id=members.id
                 AND users.id=members.user_id
                 AND roles.id=member_roles.role_id
                 AND users.status=1
                 AND login=?
                 AND identifier=? ";
-:0c83d98252d9
+    $self->{SoundSoftwareQuery} = trim($query);
-:3c16ed8faa07
+            Chris
 sub SoundSoftwareDbUser { set_val('SoundSoftwareDbUser', @_); }
 sub SoundSoftwareDbPass { set_val('SoundSoftwareDbPass', @_); }
 sub SoundSoftwareDbWhereClause {
-:0c83d98252d9
+    my ($self, $parms, $arg) = @_;
     $self->{SoundSoftwareQuery} = trim($self->{SoundSoftwareQuery}.($arg ? $arg : "")." ");
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+sub SoundSoftwareRepoPrefix {
     my ($self, $parms, $arg) = @_;
     if ($arg) {
 	$self->{SoundSoftwareRepoPrefix} = $arg;
+    }
-:3c16ed8faa07
+            Chris
-:897bc2b63bfe
+sub SoundSoftwareSslRequired { set_val('SoundSoftwareSslRequired', @_); }
-:3c16ed8faa07
+sub trim {
-:0c83d98252d9
+    my $string = shift;
     $string =~ s/\s{2,}/ /g;
     return $string;
-:3c16ed8faa07
+            Chris
 sub set_val {
-:0c83d98252d9
+    my ($key, $self, $parms, $arg) = @_;
     $self->{$key} = $arg;
-:3c16ed8faa07
+            Chris
 Apache2::Module::add(__PACKAGE__, \@directives);
 my %read_only_methods = map { $_ => 1 } qw/GET PROPFIND REPORT OPTIONS/;
 sub access_handler {
-:0c83d98252d9
+    my $r = shift;
-:3c16ed8faa07
+            Chris
-:bd1d512f9e1b
+    print STDERR "SoundSoftware.pm:$$: In access handler at " . scalar localtime() . "\n";
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+    unless ($r->some_auth_required) {
 	$r->log_reason("No authentication has been configured");
 	return FORBIDDEN;
+    }
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+    my $method = $r->method;
-:3c16ed8faa07
+            Chris
-:bd1d512f9e1b
+    print STDERR "SoundSoftware.pm:$$: Method: $method, uri " . $r->uri . ", location " . $r->location . "\n";
     print STDERR "SoundSoftware.pm:$$: Accept: " . $r->headers_in->{Accept} . "\n";
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+    my $dbh = connect_database($r);
-:a389c77da9fd
+    unless ($dbh) {
-:bd1d512f9e1b
+	print STDERR "SoundSoftware.pm:$$: Database connection failed!: " . $DBI::errstr . "\n";
-:a389c77da9fd
+	return FORBIDDEN;
+    }
-:034e9b00b341
+    print STDERR "Connected to db, dbh is " . $dbh . "\n";
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+    my $project_id = get_project_identifier($dbh, $r);
-:034e9b00b341
+            chris
-:897bc2b63bfe
+    # We want to delegate most of the work to the authentication
     # handler (to ensure that user is asked to login even for
     # nonexistent projects -- so they can't tell whether a private
     # project exists or not without authenticating). So
+    #
     # * if the project is public
     #   - if the method is read-only
     #     + set handler to OK, no auth needed
     #   - if the method is not read-only
     #     + if the repo is read-only, return forbidden
     #     + else require auth
     # * if the project is not public or does not exist
     #     + require auth
+    #
     # If we are requiring auth and are not currently https, and
     # https is required, then we must return a redirect to https
     # instead of an OK.
-:034e9b00b341
+            chris
-:0c83d98252d9
+    my $status = get_project_status($dbh, $project_id, $r);
-:897bc2b63bfe
+    my $readonly = project_repo_is_readonly($dbh, $project_id, $r);
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+    $dbh->disconnect();
     undef $dbh;
-:3c16ed8faa07
+            Chris
-:1d1b8170c2f7
+    my $auth_ssl_reqd = will_require_ssl_auth($r);
-:897bc2b63bfe
+    if ($status == 1) { # public
 	print STDERR "SoundSoftware.pm:$$: Project is public\n";
 	if (!defined $read_only_methods{$method}) {
 	    print STDERR "SoundSoftware.pm:$$: Method is not read-only\n";
 	    if ($readonly) {
 		print STDERR "SoundSoftware.pm:$$: Project repo is read-only, refusing access\n";
 		return FORBIDDEN;
 	    } else {
 		print STDERR "SoundSoftware.pm:$$: Project repo is read-write, auth required\n";
 		# fall through, this is the normal case
+	    }
-:1d1b8170c2f7
+        } elsif ($auth_ssl_reqd and $r->unparsed_uri =~ m/cmd=branchmap/) {
             # A hac^H^H^Hspecial case. We want to ensure we switch to
             # https (if it will be necessarily for authentication)
             # before the first POST request, and this is what I think
             # will give us suitable warning for Mercurial.
             print STDERR "SoundSoftware.pm:$$: Switching to HTTPS in preparation\n";
             # fall through, this is the normal case
-:897bc2b63bfe
+	} else {
 	    # Public project, read-only method -- this is the only
 	    # case we can decide for certain to accept in this function
 	    print STDERR "SoundSoftware.pm:$$: Method is read-only, no restriction here\n";
 	    $r->set_handlers(PerlAuthenHandler => [\&OK]);
 	    return OK;
+	}
     } else { # status != 1, i.e. nonexistent or private -- equivalent here
 	print STDERR "SoundSoftware.pm:$$: Project is private or nonexistent, auth required\n";
 	# fall through
-:0c83d98252d9
+            Chris
-:3c16ed8faa07
+            Chris
-:1d1b8170c2f7
+    if ($auth_ssl_reqd) {
         my $redir_to = "https://" . $r->hostname() . $r->unparsed_uri();
         print STDERR "SoundSoftware.pm:$$: Need to switch to HTTPS, redirecting to $redir_to\n";
         $r->headers_out->add('Location' => $redir_to);
         return REDIRECT;
-:897bc2b63bfe
+    } else {
-:1d1b8170c2f7
+        return OK;
-:897bc2b63bfe
+            Chris
-:3c16ed8faa07
+            Chris
 sub authen_handler {
-:0c83d98252d9
+    my $r = shift;
-:bd1d512f9e1b
+    print STDERR "SoundSoftware.pm:$$: In authentication handler at " . scalar localtime() . "\n";
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+    my $dbh = connect_database($r);
-:a389c77da9fd
+    unless ($dbh) {
-:bd1d512f9e1b
+        print STDERR "SoundSoftware.pm:$$: Database connection failed!: " . $DBI::errstr . "\n";
-:a389c77da9fd
+        return AUTH_REQUIRED;
+    }
-:0c83d98252d9
+            Chris
     my $project_id = get_project_identifier($dbh, $r);
     my $realm = get_realm($dbh, $project_id, $r);
     $r->auth_name($realm);
     my ($res, $redmine_pass) =  $r->get_basic_auth_pw();
     unless ($res == OK) {
 	$dbh->disconnect();
 	undef $dbh;
 	return $res;
+    }
-:bd1d512f9e1b
+    print STDERR "SoundSoftware.pm:$$: User is " . $r->user . ", got password\n";
-:0c83d98252d9
+            Chris
-:897bc2b63bfe
+    my $status = get_project_status($dbh, $project_id, $r);
     if ($status == 0) {
 	# nonexistent, behave like private project you aren't a member of
 	print STDERR "SoundSoftware.pm:$$: Project doesn't exist, not permitted\n";
 	$dbh->disconnect();
 	undef $dbh;
 	$r->note_auth_failure();
 	return AUTH_REQUIRED;
+    }
-:0c83d98252d9
+    my $permitted = is_permitted($dbh, $project_id, $r->user, $redmine_pass, $r);
     $dbh->disconnect();
     undef $dbh;
     if ($permitted) {
 	return OK;
     } else {
-:bd1d512f9e1b
+	print STDERR "SoundSoftware.pm:$$: Not permitted\n";
-:0c83d98252d9
+	$r->note_auth_failure();
 	return AUTH_REQUIRED;
+    }
-:3c16ed8faa07
+            Chris
 sub get_project_status {
-:0c83d98252d9
+    my $dbh = shift;
-:3c16ed8faa07
+    my $project_id = shift;
     my $r = shift;
-:0c83d98252d9
+            Chris
     if (!defined $project_id or $project_id eq '') {
 	return 0; # nonexistent
+    }
-:3c16ed8faa07
+            Chris
     my $sth = $dbh->prepare(
         "SELECT is_public FROM projects WHERE projects.identifier = ?;"
     );
     $sth->execute($project_id);
-:0c83d98252d9
+    my $ret = 0; # nonexistent
-:3c16ed8faa07
+    if (my @row = $sth->fetchrow_array) {
     	if ($row[0] eq "1" || $row[0] eq "t") {
 	    $ret = 1; # public
     	} else {
-:0c83d98252d9
+	    $ret = 2; # private
-:3c16ed8faa07
+            Chris
+    }
     $sth->finish();
     undef $sth;
     $ret;
+}
-:1d1b8170c2f7
+sub will_require_ssl_auth {
     my $r = shift;
     my $cfg = Apache2::Module::get_config
         (__PACKAGE__, $r->server, $r->per_dir_config);
     if ($cfg->{SoundSoftwareSslRequired} eq "on") {
         if ($r->dir_config('HTTPS') eq "on") {
             # already have ssl
             return 0;
         } else {
             # require ssl for auth, don't have it yet
             return 1;
+        }
     } elsif ($cfg->{SoundSoftwareSslRequired} eq "off") {
         # don't require ssl for auth
         return 0;
     } else {
         print STDERR "WARNING: SoundSoftware.pm:$$: SoundSoftwareSslRequired should be either 'on' or 'off'\n";
         # this is safer
         return 1;
+    }
+}
-:034e9b00b341
+sub project_repo_is_readonly {
     my $dbh = shift;
     my $project_id = shift;
     my $r = shift;
     if (!defined $project_id or $project_id eq '') {
         return 0; # nonexistent
+    }
     my $sth = $dbh->prepare(
         "SELECT repositories.is_external FROM repositories, projects WHERE projects.identifier = ? AND repositories.project_id = projects.id;"
     );
     $sth->execute($project_id);
     my $ret = 0; # nonexistent
     if (my @row = $sth->fetchrow_array) {
-:6d3f8aeb51b7
+        if (defined($row[0]) && ($row[0] eq "1" || $row[0] eq "t")) {
-:034e9b00b341
+            $ret = 1; # read-only (i.e. external)
         } else {
             $ret = 0; # read-write
+        }
+    }
     $sth->finish();
     undef $sth;
     $ret;
+}
-:0c83d98252d9
+sub is_permitted {
     my $dbh = shift;
     my $project_id = shift;
     my $redmine_user = shift;
     my $redmine_pass = shift;
     my $r = shift;
-:3c16ed8faa07
+            Chris
-:1e9b1bdd062e
+    my $pass_digest = Digest::SHA::sha1_hex($redmine_pass);
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+    my $cfg = Apache2::Module::get_config
 	(__PACKAGE__, $r->server, $r->per_dir_config);
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+    my $query = $cfg->{SoundSoftwareQuery};
     my $sth = $dbh->prepare($query);
     $sth->execute($redmine_user, $project_id);
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+    my $ret;
-:6d3f8aeb51b7
+    while (my ($hashed_password, $salt, $auth_source_id, $permissions) = $sth->fetchrow_array) {
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+	# Test permissions for this user before we verify credentials
 	# -- if the user is not permitted this action anyway, there's
 	# not much point in e.g. contacting the LDAP
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+	my $method = $r->method;
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+	if ((defined $read_only_methods{$method} && $permissions =~ /:browse_repository/)
 	    || $permissions =~ /:commit_access/) {
 	    # User would be permitted this action, if their
 	    # credentials checked out -- test those now
 	    print STDERR "SoundSoftware.pm: User $redmine_user has required role, checking credentials\n";
 	    unless ($auth_source_id) {
-:1e9b1bdd062e
+                my $salted_password = Digest::SHA::sha1_hex($salt.$pass_digest);
-:6d3f8aeb51b7
+		if ($hashed_password eq $salted_password) {
-:0c83d98252d9
+		    print STDERR "SoundSoftware.pm: User $redmine_user authenticated via password\n";
 		    $ret = 1;
 		    last;
+		}
 	    } else {
 		my $sthldap = $dbh->prepare(
 		    "SELECT host,port,tls,account,account_password,base_dn,attr_login FROM auth_sources WHERE id = ?;"
 		    );
 		$sthldap->execute($auth_source_id);
 		while (my @rowldap = $sthldap->fetchrow_array) {
 		    my $ldap = Authen::Simple::LDAP->new(
 			host    => ($rowldap[2] eq "1" || $rowldap[2] eq "t") ? "ldaps://$rowldap[0]" : $rowldap[0],
 			port    => $rowldap[1],
 			basedn  => $rowldap[5],
 			binddn  => $rowldap[3] ? $rowldap[3] : "",
 			bindpw  => $rowldap[4] ? $rowldap[4] : "",
 			filter  => "(".$rowldap[6]."=%s)"
 			);
 		    if ($ldap->authenticate($redmine_user, $redmine_pass)) {
-:bd1d512f9e1b
+			print STDERR "SoundSoftware.pm:$$: User $redmine_user authenticated via LDAP\n";
-:0c83d98252d9
+			$ret = 1;
+		    }
+		}
 		$sthldap->finish();
 		undef $sthldap;
-:8653bddf26a6
+                last if ($ret);
-:0c83d98252d9
+            Chris
 	} else {
-:bd1d512f9e1b
+	    print STDERR "SoundSoftware.pm:$$: User $redmine_user lacks required role for this project\n";
-:0c83d98252d9
+            Chris
-:3c16ed8faa07
+            Chris
-:0c83d98252d9
+    $sth->finish();
     undef $sth;
     $ret;
-:3c16ed8faa07
+            Chris
 sub get_project_identifier {
-:0c83d98252d9
+    my $dbh = shift;
-:3c16ed8faa07
+    my $r = shift;
     my $location = $r->location;
-:1ce6efe3db0e
+    my ($repo) = $r->uri =~ m{$location/*([^/]*)};
-:2c10dc5f122d
+            Chris
     return $repo if (!$repo);
-:3c16ed8faa07
+    $repo =~ s/[^a-zA-Z0-9\._-]//g;
-:51c97efbe241
+            Chris
-:0c83d98252d9
+    # The original Redmine.pm returns the string just calculated as
     # the project identifier.  That won't do for us -- we may have
     # (and in fact already do have, in our test instance) projects
     # whose repository names differ from the project identifiers.
     # This is a rather fundamental change because it means that almost
     # every request needs more than one database query -- which
     # prompts us to start passing around $dbh instead of connecting
     # locally within each function as is done in Redmine.pm.
-:3c16ed8faa07
+    my $sth = $dbh->prepare(
         "SELECT projects.identifier FROM projects, repositories WHERE repositories.project_id = projects.id AND repositories.url LIKE ?;"
     );
-:0c83d98252d9
+    my $cfg = Apache2::Module::get_config
 	(__PACKAGE__, $r->server, $r->per_dir_config);
     my $prefix = $cfg->{SoundSoftwareRepoPrefix};
     if (!defined $prefix) { $prefix = '%/'; }
-:3c16ed8faa07
+    my $identifier = '';
-:0c83d98252d9
+    $sth->execute($prefix . $repo);
-:3c16ed8faa07
+    my $ret = 0;
     if (my @row = $sth->fetchrow_array) {
 	$identifier = $row[0];
+    }
     $sth->finish();
     undef $sth;
-:bd1d512f9e1b
+    print STDERR "SoundSoftware.pm:$$: Repository '$repo' belongs to project '$identifier'\n";
-:3c16ed8faa07
+            Chris
     $identifier;
+}
-:0c83d98252d9
+sub get_realm {
     my $dbh = shift;
     my $project_id = shift;
     my $r = shift;
     my $sth = $dbh->prepare(
         "SELECT projects.name FROM projects WHERE projects.identifier = ?;"
     );
     my $name = $project_id;
     $sth->execute($project_id);
     my $ret = 0;
     if (my @row = $sth->fetchrow_array) {
 	$name = $row[0];
+    }
     $sth->finish();
     undef $sth;
     # be timid about characters not permitted in auth realm and revert
     # to project identifier if any are found
     if ($name =~ m/[^\w\d\s\._-]/) {
 	$name = $project_id;
-:c7a731db96e5
+    } elsif ($name =~ m/^\s*$/) {
 	# empty or whitespace
 	$name = $project_id;
+    }
     if ($name =~ m/^\s*$/) {
         # nothing even in $project_id -- probably a nonexistent project.
         # use repo name instead (don't want to admit to user that project
         # doesn't exist)
         my $location = $r->location;
-:1ce6efe3db0e
+        my ($repo) = $r->uri =~ m{$location/*([^/]*)};
-:c7a731db96e5
+        $name = $repo;
-:0c83d98252d9
+            Chris
-:cf4cc816278a
+#    my $realm = '"Mercurial repository for ' . "'$name'" . '"';
 # see #577:
     my $realm = '"Mercurial repository for ' . "$name" . '"';
-:0c83d98252d9
+            Chris
     $realm;
+}
-:3c16ed8faa07
+sub connect_database {
     my $r = shift;
-:0c83d98252d9
+    my $cfg = Apache2::Module::get_config
 	(__PACKAGE__, $r->server, $r->per_dir_config);
     return DBI->connect($cfg->{SoundSoftwareDSN},
-:a389c77da9fd
+	                $cfg->{SoundSoftwareDbUser},
 		        $cfg->{SoundSoftwareDbPass});
-:3c16ed8faa07
+            Chris
 ;
-:ed8222a04634
+#!/usr/bin/env ruby
 # == Synopsis
+#
-:7658d21a1493
+# convert-external-repos: Update local Mercurial mirrors of external repos,
 # by running an external command for each project requiring an update.
-:ed8222a04634
+            chris
 # == Usage
+#
 #    convert-external-repos [OPTIONS...] -s [DIR] -r [HOST]
+#
 # == Arguments (mandatory)
+#
-:7658d21a1493
+#   -s, --scm-dir=DIR         use DIR as base directory for repositories
-:ed8222a04634
+#   -r, --redmine-host=HOST   assume Redmine is hosted on HOST. Examples:
 #                             -r redmine.example.net
 #                             -r http://redmine.example.net
 #                             -r https://example.net/redmine
 #   -k, --key=KEY             use KEY as the Redmine API key
-:7658d21a1493
+#   -c, --command=COMMAND     use this command to update each external
 #                             repository: command is called with the name
 #                             of the project, the path to its repo, and
 #                             its external repo url as its three args
-:ed8222a04634
+            chris
 # == Options
+#
 #   --http-user=USER          User for HTTP Basic authentication with Redmine WS
 #   --http-pass=PASSWORD      Password for Basic authentication with Redmine WS
 #   -t, --test                only show what should be done
 #   -h, --help                show help and exit
 #   -v, --verbose             verbose
 #   -V, --version             print version and exit
 #   -q, --quiet               no log
 require 'getoptlong'
 require 'find'
 require 'etc'
 Version = "1.0"
 opts = GetoptLong.new(
-:7658d21a1493
+                      ['--scm-dir',      '-s', GetoptLong::REQUIRED_ARGUMENT],
-:ed8222a04634
+                      ['--redmine-host', '-r', GetoptLong::REQUIRED_ARGUMENT],
                       ['--key',          '-k', GetoptLong::REQUIRED_ARGUMENT],
                       ['--http-user',          GetoptLong::REQUIRED_ARGUMENT],
                       ['--http-pass',          GetoptLong::REQUIRED_ARGUMENT],
-:7658d21a1493
+                      ['--command' ,     '-c', GetoptLong::REQUIRED_ARGUMENT],
-:ed8222a04634
+                      ['--test',         '-t', GetoptLong::NO_ARGUMENT],
                       ['--verbose',      '-v', GetoptLong::NO_ARGUMENT],
                       ['--version',      '-V', GetoptLong::NO_ARGUMENT],
                       ['--help'   ,      '-h', GetoptLong::NO_ARGUMENT],
                       ['--quiet'  ,      '-q', GetoptLong::NO_ARGUMENT]
+                      )
 $verbose      = 0
 $quiet        = false
 $redmine_host = ''
 $repos_base   = ''
 $http_user    = ''
 $http_pass    = ''
 $test         = false
-:102056ec2de9
+$mirrordir    = '/var/mirror'
-:ed8222a04634
+def log(text, options={})
   level = options[:level] || 0
   puts text unless $quiet or level > $verbose
   exit 1 if options[:exit]
 end
 def system_or_raise(command)
   raise "\"#{command}\" failed" unless system command
 end
 begin
   opts.each do |opt, arg|
     case opt
-:7658d21a1493
+    when '--scm-dir';        $repos_base   = arg.dup
-:ed8222a04634
+    when '--redmine-host';   $redmine_host = arg.dup
     when '--key';            $api_key      = arg.dup
     when '--http-user';      $http_user    = arg.dup
     when '--http-pass';      $http_pass    = arg.dup
-:7658d21a1493
+    when '--command';        $command      = arg.dup
-:ed8222a04634
+    when '--verbose';        $verbose += 1
     when '--test';           $test = true
     when '--version';        puts Version; exit
-:b61a51fb42b9
+    when '--help';           puts "Read source for documentation"; exit
-:ed8222a04634
+    when '--quiet';          $quiet = true
     end
   end
 rescue
   exit 1
 end
 if $test
   log("running in test mode")
 end
-:7658d21a1493
+if ($redmine_host.empty? or $repos_base.empty? or $command.empty?)
-:b61a51fb42b9
+  puts "Read source for documentation"; exit
-:ed8222a04634
+end
 unless File.directory?($repos_base)
   log("directory '#{$repos_base}' doesn't exist", :exit => true)
 end
 begin
   require 'active_resource'
 rescue LoadError
   log("This script requires activeresource.\nRun 'gem install activeresource' to install it.", :exit => true)
 end
 class Project < ActiveResource::Base
   self.headers["User-agent"] = "SoundSoftware external repository converter/#{Version}"
-:b61a51fb42b9
+  self.format = :xml
-:ed8222a04634
+end
 log("querying Redmine for projects...", :level => 1);
 $redmine_host.gsub!(/^/, "http://") unless $redmine_host.match("^https?://")
 $redmine_host.gsub!(/\/$/, '')
 Project.site = "#{$redmine_host}/sys";
 Project.user = $http_user;
 Project.password = $http_pass;
 begin
   # Get all active projects that have the Repository module enabled
   projects = Project.find(:all, :params => {:key => $api_key})
-:b61a51fb42b9
+rescue ActiveResource::ForbiddenAccess
   log("Request was denied by your Redmine server. Make sure that 'WS for repository management' is enabled in application settings and that you provided the correct API key.")
-:ed8222a04634
+rescue => e
   log("Unable to connect to #{Project.site}: #{e}", :exit => true)
 end
 if projects.nil?
   log('no project found, perhaps you forgot to "Enable WS for repository management"', :exit => true)
 end
 log("retrieved #{projects.size} projects", :level => 1)
 projects.each do |project|
   log("treating project #{project.name}", :level => 1)
   if project.identifier.empty?
     log("\tno identifier for project #{project.name}")
     next
-:0c7b3bb73517
+  elsif not project.identifier.match(/^[a-z0-9_\-]+$/)
-:ed8222a04634
+    log("\tinvalid identifier for project #{project.name} : #{project.identifier}");
     next
   end
   if !project.respond_to?(:repository) or !project.repository.is_external?
     log("\tproject #{project.identifier} does not use an external repository");
     next
   end
   external_url = project.repository.external_url;
   log("\tproject #{project.identifier} has external repository url #{external_url}");
   if !external_url.match(/^[a-z][a-z+]{0,8}[a-z]:\/\//)
     log("\tthis doesn't look like a plausible url to me, skipping")
     next
   end
   repos_path = File.join($repos_base, project.identifier).gsub(File::SEPARATOR, File::ALT_SEPARATOR || File::SEPARATOR)
-:7658d21a1493
+  unless File.directory?(repos_path)
     log("\tproject repo directory '#{repos_path}' doesn't exist")
-:ed8222a04634
+    next
   end
-:7658d21a1493
+  system($command, project.identifier, repos_path, external_url)
-:102056ec2de9
+            chris
   $cache_clearance_file = File.join($mirrordir, project.identifier, 'url_changed')
   if File.file?($cache_clearance_file)
     log("\tproject repo url has changed, requesting cache clearance")
     if project.post(:repository_cache, :key => $api_key)
       File.delete($cache_clearance_file)
     end
   end
-:ed8222a04634
+            chris
 end
-:87bea4981d6d
+#!/usr/bin/env ruby
 # Create authormap files for hg repos based on the changeset & project
 # member info available to Redmine.
+#
 # We have a set of hg repos in a given directory:
+#
 # /var/hg/repo_1
 # /var/hg/repo_2
 # /var/hg/repo_3
+#
 # and we want to produce authormap files in another directory:
+#
 # /var/repo-export/authormap/authormap_repo_1
 # /var/repo-export/authormap/authormap_repo_2
 # /var/repo-export/authormap/authormap_repo_3
+#
 # This script does that, if given the two directory names as arguments
 # to the -s and -o options. In the above example:
+#
-:05d639e5d59b
+# ./script/rails runner -e production extra/soundsoftware/create-repo-authormaps.rb -s /var/hg -o /var/repo-export/authormap
-:87bea4981d6d
+            Chris
 # Note that this script will overwrite any existing authormap
 # files. (That's why the output files are given an authormap_ prefix,
 # so we're less likely to clobber something else if the user gets the
 # arguments wrong.)
 require 'getoptlong'
 opts = GetoptLong.new(
-:05d639e5d59b
+                      ['--scm-dir', '-s', GetoptLong::REQUIRED_ARGUMENT],
                       ['--out-dir', '-o', GetoptLong::REQUIRED_ARGUMENT],
                       ['--environment', '-e', GetoptLong::OPTIONAL_ARGUMENT]
-:87bea4981d6d
+            Chris
 $repos_base   = ''
 $out_base     = ''
 def usage
   puts "See source code for supported options"
   exit
 end
 begin
   opts.each do |opt, arg|
     case opt
     when '--scm-dir';   $repos_base   = arg.dup
     when '--out-dir';   $out_base     = arg.dup
     end
   end
 rescue
   exit 1
 end
 if ($repos_base.empty? or $out_base.empty?)
   usage
 end
 unless File.directory?($repos_base)
-:322d7b57e5f0
+  puts "input directory '#{$repos_base}' doesn't exist"
   exit 1
-:87bea4981d6d
+end
 unless File.directory?($out_base)
-:322d7b57e5f0
+  puts "output directory '#{$out_base}' doesn't exist"
   exit 1
-:87bea4981d6d
+end
 projects = Project.find(:all)
 if projects.nil?
-:322d7b57e5f0
+  puts 'No projects found'
   exit 1
-:87bea4981d6d
+end
 projects.each do |proj|
-:fd4cc11ae096
+            Chris
   next unless proj.is_public
-:87bea4981d6d
+  next unless proj.respond_to?(:repository)
   repo = proj.repository
-:22d57b0e0a77
+  next if repo.nil? or repo.url.empty?
-:87bea4981d6d
+            Chris
   repo_url = repo.url
   repo_url = repo_url.gsub(/^file:\/*/, "/");
   if repo_url != File.join($repos_base, proj.identifier)
-:60acfbd8f6d6
+    puts "Project #{proj.identifier} has repo in unsupported location #{repo_url}, skipping"
-:87bea4981d6d
+    next
   end
-:60acfbd8f6d6
+  committers = repo.committers
-:87bea4981d6d
+            Chris
   authormap = ""
-:60acfbd8f6d6
+  committers.each do |c, uid|
-:3a2254124fa8
+            Chris
     # Some of our repos have broken email addresses in them: e.g. one
     # changeset has a committer name of the form
+    #
     # NAME <name <NAME <name@example.com">
+    #
     # I don't know how it got like that... If the committer has more
     # than one '<' in it, truncate it just before the first one, and
     # then we look up the author name again.
     if c =~ /<.*</ then
       c = c.sub(/\s*<.*$/, "")
     end
-:87bea4981d6d
+    if not c =~ /[^<]+<.*@.*>/ then
-:60acfbd8f6d6
+      user = User.find_by_id uid
-:22d57b0e0a77
+      authormap << "#{c}=#{user.name} <#{user.mail}>\n" unless user.nil?
-:87bea4981d6d
+    end
   end
-:22d57b0e0a77
+  File.open(File.join($out_base, "authormap_#{proj.identifier}"), "w") do |f|
-:87bea4981d6d
+    f.puts(authormap)
   end
 end
-:5b028aef59a7
+#!/usr/bin/perl -w
 # Read a Doxyfile and print it out again to stdout, with only
 # whitelisted keys in it and with some keys set to pre-fixed values.
+#
 # Note that OUTPUT_DIRECTORY is not included; it should be added by
 # the caller
 use strict;
 my $txt = join "", <>;
 $txt =~ s/^\s*#.*$//gm;
 $txt =~ s/\\\n//gs;
 $txt =~ s/\r//g;
 $txt =~ s/\n\s*\n/\n/gs;
 my %fixed = (
     FULL_PATH_NAMES => "NO",
     SYMBOL_CACHE_SIZE => 2,
     EXCLUDE_SYMLINKS => "YES",
     GENERATE_HTML => "YES",
     PERL_PATH => "/usr/bin/perl",
     HAVE_DOT => "YES",
     HTML_OUTPUT => ".",
-:3c084a25d8ab
+    HTML_DYNAMIC_SECTIONS => "NO",
-:5b028aef59a7
+    SEARCHENGINE => "NO",
     DOT_FONTNAME => "FreeMono",
     DOT_FONTSIZE => 10,
     DOT_FONTPATH => "/usr/share/fonts/truetype/freefont",
     DOT_IMAGE_FORMAT => "png",
     DOT_PATH => "/usr/bin/dot",
     DOT_TRANSPARENT => "YES",
 );
-:df89e7aa3ce8
+# These are the keys that are safe to take from the output and include
 # in the output; they may still need to be checked for safe values (if
 # file paths).
-:5b028aef59a7
+my @safe = qw(
-:df89e7aa3ce8
+INPUT
 FILE_PATTERNS
 EXAMPLE_PATH
 EXAMPLE_PATTERNS
 IMAGE_PATH
 INCLUDE_PATH
 INCLUDE_FILE_PATTERNS
-:5b028aef59a7
+DOXYFILE_ENCODING
 PROJECT_NAME
 PROJECT_NUMBER
 CREATE_SUBDIRS
 OUTPUT_LANGUAGE
 BRIEF_MEMBER_DESC
 REPEAT_BRIEF
 ABBREVIATE_BRIEF
 ALWAYS_DETAILED_SEC
 INLINE_INHERITED_MEMB
 STRIP_FROM_PATH
 STRIP_FROM_INC_PATH
 JAVADOC_AUTOBRIEF
 QT_AUTOBRIEF
 MULTILINE_CPP_IS_BRIEF
 INHERIT_DOCS
 SEPARATE_MEMBER_PAGES
 TAB_SIZE
 ALIASES
 OPTIMIZE_OUTPUT_FOR_C
 OPTIMIZE_OUTPUT_JAVA
 OPTIMIZE_FOR_FORTRAN
 OPTIMIZE_OUTPUT_VHDL
 EXTENSION_MAPPING
 BUILTIN_STL_SUPPORT
 CPP_CLI_SUPPORT
 SIP_SUPPORT
 IDL_PROPERTY_SUPPORT
 DISTRIBUTE_GROUP_DOC
 SUBGROUPING
 TYPEDEF_HIDES_STRUCT
 EXTRACT_ALL
 EXTRACT_PRIVATE
 EXTRACT_STATIC
 EXTRACT_LOCAL_CLASSES
 EXTRACT_LOCAL_METHODS
 EXTRACT_ANON_NSPACES
 HIDE_UNDOC_MEMBERS
 HIDE_UNDOC_CLASSES
 HIDE_FRIEND_COMPOUNDS
 HIDE_IN_BODY_DOCS
 INTERNAL_DOCS
 HIDE_SCOPE_NAMES
 SHOW_INCLUDE_FILES
 FORCE_LOCAL_INCLUDES
 INLINE_INFO
 SORT_MEMBER_DOCS
 SORT_BRIEF_DOCS
 SORT_MEMBERS_CTORS_1ST
 SORT_GROUP_NAMES
 SORT_BY_SCOPE_NAME
 GENERATE_TODOLIST
 GENERATE_TESTLIST
 GENERATE_BUGLIST
 GENERATE_DEPRECATEDLIST
 ENABLED_SECTIONS
 MAX_INITIALIZER_LINES
 SHOW_USED_FILES
 SHOW_DIRECTORIES
 SHOW_FILES
 SHOW_NAMESPACES
 QUIET
 WARNINGS
 WARN_IF_UNDOCUMENTED
 WARN_IF_DOC_ERROR
 WARN_NO_PARAMDOC
 INPUT_ENCODING
 RECURSIVE
 EXCLUDE
 EXCLUDE_SYMLINKS
 EXCLUDE_PATTERNS
 EXCLUDE_SYMBOLS
 EXAMPLE_RECURSIVE
 SOURCE_BROWSER
 INLINE_SOURCES
 STRIP_CODE_COMMENTS
 REFERENCED_BY_RELATION
 REFERENCES_RELATION
 REFERENCES_LINK_SOURCE
 VERBATIM_HEADERS
 ALPHABETICAL_INDEX
 COLS_IN_ALPHA_INDEX
 IGNORE_PREFIX
 HTML_TIMESTAMP
 HTML_ALIGN_MEMBERS
 ENABLE_PREPROCESSING
 MACRO_EXPANSION
 EXPAND_ONLY_PREDEF
 SEARCH_INCLUDES
 PREDEFINED
 EXPAND_AS_DEFINED
 SKIP_FUNCTION_MACROS
 ALLEXTERNALS
 EXTERNAL_GROUPS
 CLASS_DIAGRAMS
 HIDE_UNDOC_RELATIONS
 CLASS_GRAPH
 COLLABORATION_GRAPH
 GROUP_GRAPHS
 UML_LOOK
 TEMPLATE_RELATIONS
 INCLUDE_GRAPH
 INCLUDED_BY_GRAPH
 CALL_GRAPH
 CALLER_GRAPH
 GRAPHICAL_HIERARCHY
 DIRECTORY_GRAPH
 DOT_GRAPH_MAX_NODES
 MAX_DOT_GRAPH_DEPTH
 DOT_MULTI_TARGETS
 DOT_CLEANUP
 );
 my %safehash;
 for my $sk (@safe) { $safehash{$sk} = 1; }
 my @lines = split "\n", $txt;
 my %settings;
 sub is_safe {
     my $key = shift;
     defined $safehash{$key} and $safehash{$key} == 1;
+}
 sub has_file_path {
     # Returns true if the given key expects a file path as a value.
     # We only need to test keys that are safe; unsafe keys have been
     # rejected already.
     my $key = shift;
     $key eq "INPUT" or
 	$key =~ /^OUTPUT_/ or
 	$key =~ /_PATH$/ or
 	$key =~ /_PATTERNS$/;
+}
 sub is_safe_file_path {
     my $value = shift;
     not $value =~ /^\// and not $value =~ /\.\./;
+}
 foreach my $line (@lines) {
     chomp $line;
     my ($key, $value) = split /\s*=\s*/, $line;
     next if !defined $key;
     if ($key =~ /^GENERATE_/ and not $key =~ /LIST$/) {
 	print STDERR "NOTE: Setting $key explicitly to NO\n";
 	$settings{$key} = "NO";
 	next;
+    }
     if (!is_safe($key)) {
 	print STDERR "NOTE: Skipping non-whitelisted key $key\n";
 	next;
+    }
     if (has_file_path($key) and !is_safe_file_path($value)) {
 	print STDERR "ERROR: Unsafe file path \"$value\" for key $key\n";
 	exit 1;
+    }
     $settings{$key} = $value;
+}
-:3c084a25d8ab
+foreach my $key (keys %fixed) {
     my $value = $fixed{$key};
     print STDERR "NOTE: Setting $key to fixed value $value\n";
     $settings{$key} = $value;
+}
-:5b028aef59a7
+print join "\n", map { "$_ = $settings{$_}" } keys %settings;
 print "\n";
-:05d639e5d59b
+#!/bin/bash
 set -e
 progdir=$(dirname $0)
 case "$progdir" in
     /*) ;;
     *) progdir="$(pwd)/$progdir" ;;
 esac
 rails_scriptdir="$progdir/../../script"
 rails="$rails_scriptdir/rails"
 if [ ! -x "$rails" ]; then
     echo "Expected to find rails executable at $rails"
     exit 2
 fi
 fastexport="$progdir/../fast-export/hg-fast-export.sh"
 if [ ! -x "$fastexport" ]; then
     echo "Expected to find hg-fast-export.sh executable at $fastexport"
     exit 2
 fi
-:248c402992ba
+environment="$1"
 hgdir="$2"
 gitdir="$3"
-:05d639e5d59b
+            Chris
 if [ -z "$hgdir" ] || [ -z "$gitdir" ]; then
-:248c402992ba
+    echo "Usage: $0 <environment> <hgdir> <gitdir>"
     echo "  where"
     echo "  - environment is the Rails environment (development or production)"
     echo "  - hgdir is the directory containing project Mercurial repositories"
     echo "  - gitdir is the directory in which output git repositories are to be"
     echo "    created or updated"
-:05d639e5d59b
+    exit 2
 fi
 if [ ! -d "$hgdir" ]; then
     echo "Mercurial repository directory $hgdir not found"
     exit 1
 fi
 if [ ! -d "$gitdir" ]; then
     echo "Target git repository dir $gitdir not found (please create at least the empty directory)"
     exit 1
 fi
 set -u
-:7d825cbd76c8
+authordir="$gitdir/__AUTHORMAPS"
-:05d639e5d59b
+mkdir -p "$authordir"
-:7d825cbd76c8
+wastedir="$gitdir/__WASTE"
 mkdir -p "$wastedir"
-:bca3b5e5bbf2
+echo "Extracting author maps..."
-:248c402992ba
+            Chris
-:7d825cbd76c8
+# Delete any existing authormap files, because we want to ensure we
 # don't have an authormap for any project that was exportable but has
 # become non-exportable (e.g. has gone private)
-:36dddb6755f6
+rm -f "$authordir/*"
-:7d825cbd76c8
+            Chris
-:248c402992ba
+"$rails" runner -e "$environment" "$progdir/create-repo-authormaps.rb" \
-:05d639e5d59b
+	 -s "$hgdir" -o "$authordir"
 for hgrepo in "$hgdir"/*; do
     if [ ! -d "$hgrepo/.hg" ]; then
 	echo "Directory $hgrepo does not appear to be a Mercurial repo, skipping"
 	continue
     fi
     reponame=$(basename "$hgrepo")
     authormap="$authordir/authormap_$reponame"
     gitrepo="$gitdir/$reponame"
     if [ ! -f "$authormap" ]; then
-:bca3b5e5bbf2
+	echo "No authormap file was created for repo $reponame, skipping"
-:7d825cbd76c8
+            Chris
 	# If there is no authormap file, then we should not have a git
 	# mirror -- this is a form of access control, not just an
 	# optimisation (authormap files are expected to exist for all
 	# exportable projects, even if empty). So if a git mirror
 	# exists, we move it away
 	if [ -d "$gitrepo" ]; then
 	    mv "$gitrepo" "$wastedir/$(date +%s).$reponame"
 	fi
-:05d639e5d59b
+	continue
     fi
     if [ ! -d "$gitrepo" ]; then
 	git init "$gitrepo"
     fi
-:bca3b5e5bbf2
+    echo
-:248c402992ba
+    echo "About to run fast export for repo $reponame..."
-:05d639e5d59b
+            Chris
+    (
 	cd "$gitrepo"
-:28cde511f312
+            Chris
         # Force is necessary because git-fast-import (or git) can't handle
         # branches having more than one head ("Error: repository has at
         # least one unnamed head"), which happens from time to time in
         # valid Hg repos. With --force apparently it will just pick one
         # of the two heads arbitrarily, which is also alarming but is
         # more likely to be useful
 	"$fastexport" --quiet -r "$hgrepo" -A "$authormap" --hg-hash --force
-:05d639e5d59b
+            Chris
     echo "Fast export done"
 done
 echo "All done"
-:1e55195bca45
+#!/bin/bash
 # Run this script from anywhere
 # Enumerate Hg repos; make sure they're up to date; extract docs for
 # each
 hgdir="/var/hg"
 docdir="/var/doc"
-:c3544e9fd588
+logfile="/var/www/test-cannam/log/extract-docs.log"
 redgrp="redmine"
-:1e55195bca45
+            chris
-:292cde42265a
+apikey=""
-:5410d82c12df
+apischeme="https"
-:292cde42265a
+apihost=""
 apiuser=""
 apipass=""
-:1e55195bca45
+progdir=$(dirname $0)
 case "$progdir" in
     /*) ;;
     *) progdir="$(pwd)/$progdir" ;;
 esac
-:e7ba81c8dc5a
+types="doxygen javadoc matlabdocs" # Do Doxygen first (it can be used for Java too)
-:1e55195bca45
+            chris
 for x in $types; do
     if [ ! -x "$progdir/extract-$x.sh" ]; then
 	echo "Helper script not available: $progdir/extract-$x.sh"
 	exit 1
     fi
 done
-:292cde42265a
+enable_embedded()
+{
     p="$1"
-:3c084a25d8ab
+    if [ -n "$apikey" ]; then
 	if [ -n "$apiuser" ]; then
-:5410d82c12df
+	    sudo -u docgen curl -u "$apiuser":"$apipass" "$apischeme://$apihost/sys/projects/$p/embedded.xml?enable=1&key=$apikey" -d ""
-:3c084a25d8ab
+	else
-:5410d82c12df
+	    sudo -u docgen curl "$apischeme://$apihost/sys/projects/$p/embedded.xml?enable=1&key=$apikey" -d ""
-:3c084a25d8ab
+	fi
     else
 	echo "Can't enable Embedded, API not configured" 1>&2
-:292cde42265a
+    fi
+}
-:c3544e9fd588
+# We want to ensure the doc extraction is done by the unprivileged
 # user docgen, which is not a member of any interesting group
+#
 # To this end, we create the tmpdir with user docgen and group
 # www-data, and use the www-data user to pull out an archive of the Hg
 # repo tip into a location beneath that, before using the docgen user
 # to extract docs from that location and write them into the tmpdir
 # Same tmpdir for each project: we delete and recreate to avoid
 # cleanup duty from lots of directories being created
+#
 tmpdir=$(mktemp -d "$docdir/tmp_XXXXXX")
 fail()
+{
     message="$1"
     echo "$message" 1>&2
     case "$tmpdir" in
 	*/tmp*) rm -rf "$tmpdir";;
 	*);;
     esac
     exit 1
+}
 case "$tmpdir" in
     /*) ;;
     *) fail "Temporary directory creation failed";;
 esac
 chown docgen.www-data "$tmpdir" || fail "Temporary directory ownership change failed"
 chmod g+rwx "$tmpdir" || fail "Temporary directory permissions change failed"
-:1e55195bca45
+for projectdir in "$hgdir"/* ; do
     if [ -d "$projectdir" ] && [ -d "$projectdir/.hg" ]; then
-:c3544e9fd588
+	if ! sudo -u www-data hg -R "$projectdir" -q update; then
 	    echo "Failed to update Hg in $projectdir, skipping" 1>&2
 	    continue
 	fi
-:1e55195bca45
+	project=$(basename "$projectdir")
-:c3544e9fd588
+	tmptargetdir="$tmpdir/doc"
 	snapshotdir="$tmpdir/hgsnapshot"
-:1e55195bca45
+            chris
-:c3544e9fd588
+	rm -rf "$tmptargetdir" "$snapshotdir"
-:5b028aef59a7
+	mkdir -m 770 "$tmptargetdir" || fail "Temporary target directory creation failed"
 	chown docgen.www-data "$tmptargetdir" || fail "Temporary target directory ownership change failed"
-:c3544e9fd588
+            chris
 	mkdir -m 770 "$snapshotdir" || fail "Snapshot directory creation failed"
 	chown docgen.www-data "$snapshotdir" || fail "Snapshot directory ownership change failed"
 	hgparents=$(sudo -u www-data hg -R "$projectdir" parents)
 	if [ -z "$hgparents" ]; then
 	    echo "Hg repo at $projectdir has no working copy (empty repo?), skipping"
 	    continue
 	else
 	    echo "Found non-empty Hg repo: $projectdir for project $project"
 	fi
 	if ! sudo -u www-data hg -R "$projectdir" archive -r tip -t files "$snapshotdir"; then
 	    echo "Failed to pick archive from $projectdir, skipping" 1>&2
 	    continue
 	fi
-:1e55195bca45
+            chris
 	targetdir="$docdir/$project"
-:c3544e9fd588
+	echo "Temporary dir is $tmpdir, temporary doc dir is $tmptargetdir, snapshot dir is $snapshotdir, eventual target is $targetdir"
-:1e55195bca45
+            chris
 	for x in $types; do
-:5b028aef59a7
+	    if sudo -u docgen "$progdir/extract-$x.sh" "$project" "$snapshotdir" "$tmptargetdir" >> "$logfile" 2>&1; then
 		break
 	    else
-:1e55195bca45
+		echo "Failed to extract via type $x"
 	    fi
 	done
-:c3544e9fd588
+        if [ -f "$tmptargetdir/index.html" ]; then
-:1e55195bca45
+	    echo "Processing resulted in an index.html being created, looks good!"
 	    if [ ! -d "$targetdir" ] || [ ! -f "$targetdir/index.html" ]; then
-:c3544e9fd588
+		echo "This project hasn't had doc extracted before: enabling Embedded"
-:292cde42265a
+		enable_embedded "$project"
-:1e55195bca45
+	    fi
 	    if [ -d "$targetdir" ]; then
 		mv "$targetdir" "$targetdir"_"$$" && \
-:c3544e9fd588
+		    mv "$tmptargetdir" "$targetdir" && \
-:1e55195bca45
+		    rm -rf "$targetdir"_"$$"
-:c3544e9fd588
+		chgrp -R "$redgrp" "$targetdir"
-:1e55195bca45
+	    else
-:c3544e9fd588
+		mv "$tmptargetdir" "$targetdir"
 		chgrp -R "$redgrp" "$targetdir"
-:1e55195bca45
+	    fi
-:3c084a25d8ab
+	else
 	    echo "Processing did not result in an index.html being created"
-:1e55195bca45
+	fi
     fi
 done
-:c3544e9fd588
+rm -rf "$tmpdir"
-:1e55195bca45
+#!/bin/bash
 docdir="/var/doc"
-:3c084a25d8ab
+progdir=$(dirname $0)
 case "$progdir" in
     /*) ;;
     *) progdir="$(pwd)/$progdir" ;;
 esac
-:1e55195bca45
+project="$1"
-:c3544e9fd588
+projectdir="$2"
 targetdir="$3"
-:1e55195bca45
+            chris
-:c3544e9fd588
+if [ -z "$project" ] || [ -z "$targetdir" ] || [ -z "$projectdir" ]; then
     echo "Usage: $0 <project> <projectdir> <targetdir>"
-:1e55195bca45
+    exit 2
 fi
-:c3544e9fd588
+if [ ! -d "$projectdir" ]; then
     echo "Project directory $projectdir not found"
-:1e55195bca45
+    exit 1
 fi
 if [ ! -d "$targetdir" ]; then
     echo "Target dir $targetdir not found"
     exit 1
 fi
 if [ -f "$targetdir/index.html" ]; then
     echo "Target dir $targetdir already contains index.html"
     exit 1
 fi
 doxyfile=$(find "$projectdir" -type f -name Doxyfile -print | head -1)
 if [ -z "$doxyfile" ]; then
     echo "No Doxyfile found for project $project"
     exit 1
 fi
 echo "Project $project contains a Doxyfile at $doxyfile"
 cd "$projectdir" || exit 1
-:3c084a25d8ab
+"$progdir/doxysafe.pl" "$doxyfile" | \
     sed -e '$a OUTPUT_DIRECTORY='"$targetdir" | \
-:1e55195bca45
+    doxygen -
 #!/bin/bash
-:c1e9f2dab1d5
+            chris
-:1e55195bca45
+docdir="/var/doc"
-:c1e9f2dab1d5
+            chris
-:1e55195bca45
+project="$1"
-:c3544e9fd588
+projectdir="$2"
 targetdir="$3"
-:c1e9f2dab1d5
+            chris
-:c3544e9fd588
+if [ -z "$project" ] || [ -z "$targetdir" ] || [ -z "$projectdir" ]; then
     echo "Usage: $0 <project> <projectdir> <targetdir>"
-:1e55195bca45
+    exit 2
-:c1e9f2dab1d5
+fi
-:c3544e9fd588
+if [ ! -d "$projectdir" ]; then
     echo "Project directory $projectdir not found"
-:1e55195bca45
+    exit 1
 fi
-:c1e9f2dab1d5
+            chris
-:1e55195bca45
+if [ ! -d "$targetdir" ]; then
     echo "Target dir $targetdir not found"
     exit 1
 fi
-:c1e9f2dab1d5
+            chris
-:1e55195bca45
+if [ -f "$targetdir/index.html" ]; then
     echo "Target dir $targetdir already contains index.html"
     exit 1
-:2cec5c53cd68
+fi
-:c1e9f2dab1d5
+            chris
-:0d1c6fa50d3a
+# Identify Java files whose packages match the trailing parts of their
 # paths, and list the resulting packages and the path prefixes with
 # the packages removed (so as to find code in subdirs,
 # e.g. src/com/example/...)
 # Regexp match is very rough; check what is actually permitted for
 # package declarations
-:1e55195bca45
+find "$projectdir" -type f -name \*.java \
-:3549525ba22a
+    -exec egrep '^ *package +[a-zA-Z][a-zA-Z0-9\._-]*;.*$' \{\} /dev/null \; |
     sed -e 's/\/[^\/]*: *package */:/' -e 's/;.*$//' |
-:0d1c6fa50d3a
+    sort | uniq | (
 	current_prefix=
 	current_packages=
 	while IFS=: read filepath package; do
 	    echo "Looking at $package in $filepath"
 	    packagepath=${package//./\/}
 	    prefix=${filepath%$packagepath}
-:1e55195bca45
+	    prefix=${prefix:=$projectdir}
-:0d1c6fa50d3a
+	    if [ "$prefix" = "$filepath" ]; then
 		echo "Package $package does not match suffix of path $filepath, skipping"
 		continue
 	    fi
 	    if [ "$prefix" != "$current_prefix" ]; then
-:73401a15037b
+		echo "Package $package matches file path and has new prefix $prefix"
-:0d1c6fa50d3a
+		if [ -n "$current_packages" ]; then
 		    echo "Running Javadoc for packages $current_packages from prefix $current_prefix"
-:73401a15037b
+		    echo "Command is: javadoc -sourcepath "$current_prefix" -d "$targetdir" -subpackages $current_packages"
-:1e55195bca45
+		    javadoc -sourcepath "$current_prefix" -d "$targetdir" -subpackages $current_packages
-:0d1c6fa50d3a
+		fi
 		current_prefix="$prefix"
-:73401a15037b
+		current_packages="$package"
-:0d1c6fa50d3a
+	    else
-:73401a15037b
+		echo "Package $package matches file path with same prefix as previous file"
-:0d1c6fa50d3a
+		current_packages="$current_packages $package"
 	    fi
 	done
-:1e55195bca45
+	prefix=${prefix:=$projectdir}
-:0d1c6fa50d3a
+	if [ -n "$current_packages" ]; then
 	    echo "Running Javadoc for packages $current_packages in prefix $current_prefix"
-:73401a15037b
+  	    echo "Command is: javadoc -sourcepath "$current_prefix" -d "$targetdir" -subpackages $current_packages"
-:1e55195bca45
+	    javadoc -sourcepath "$current_prefix" -d "$targetdir" -subpackages $current_packages
-:0d1c6fa50d3a
+	fi
+    )
-:73401a15037b
+if [ -f "$targetdir"/overview-tree.html ]; then
     cp "$targetdir"/overview-tree.html "$targetdir"/index.html
 fi
-:1e55195bca45
+# for exit code:
 [ -f "$targetdir/index.html" ]
-:c1e9f2dab1d5
+            chris
-:e7ba81c8dc5a
+#!/bin/bash
 docdir="/var/doc"
 progdir=$(dirname $0)
 case "$progdir" in
     /*) ;;
     *) progdir="$(pwd)/$progdir" ;;
 esac
 project="$1"
 projectdir="$2"
 targetdir="$3"
 if [ -z "$project" ] || [ -z "$targetdir" ] || [ -z "$projectdir" ]; then
     echo "Usage: $0 <project> <projectdir> <targetdir>"
     exit 2
 fi
 if [ ! -d "$projectdir" ]; then
     echo "Project directory $projectdir not found"
     exit 1
 fi
 if [ ! -d "$targetdir" ]; then
     echo "Target dir $targetdir not found"
     exit 1
 fi
 if [ -f "$targetdir/index.html" ]; then
     echo "Target dir $targetdir already contains index.html"
     exit 1
 fi
 mfile=$(find "$projectdir" -type f -name \*.m -print0 | xargs -0 grep -l '^% ' | head -1)
 if [ -z "$mfile" ]; then
     echo "No MATLAB files with comments found for project $project"
     exit 1
 fi
 echo "Project $project contains at least one MATLAB file with comments"
 cd "$projectdir" || exit 1
 perl "$progdir/matlab-docs.pl" -c "$progdir/matlab-docs.conf" -d "$targetdir"
-:bbb88c44f805
+            Chris
-:9b4919de5317
+# Read an Apache log file in SoundSoftware site format from stdin and
 # produce some per-project stats.
-:bbb88c44f805
+            Chris
 # Invoke with e.g.
+#
 # cat /var/log/apache2/code-access.log | \
 #   script/runner -e production extra/soundsoftware/get-apache-log-stats.rb
-:198f764e734c
+            Chris
 # Use the ApacheLogRegex parser, a neat thing
 # See http://www.simonecarletti.com/blog/2009/02/apache-log-regex-a-lightweight-ruby-apache-log-parser/
 require 'apachelogregex'
 # This is the format defined in our httpd.conf
 vhost_combined_format = '%v:%p %h %{X-Forwarded-For}i %l %u %t \"%r\" %>s %O \"%{Referer}i\" \"%{User-Agent}i\"'
 parser = ApacheLogRegex.new(vhost_combined_format)
 # project name -> count of hg clones
 clones = Hash.new(0)
 # project name -> count of hg pulls
 pulls = Hash.new(0)
-:bbb88c44f805
+# project name -> count of hg pushes
 pushes = Hash.new(0)
-:198f764e734c
+            Chris
 # project name -> count of hg archive requests (i.e. Download as Zip)
 zips = Hash.new(0)
 # project name -> count of hits to pages under /projects/projectname
 hits = Hash.new(0)
-:bbb88c44f805
+# project name -> Project object
 @projects = Hash.new
-:198f764e734c
+parseable = 0
 unparseable = 0
-:56a38a9f6204
+def is_public_project?(project)
-:bbb88c44f805
+  if !project
     false
-:a97e573d7f87
+  elsif project =~ /^\d+$/
     # ignore numerical project ids, they are only used when editing projects
     false
-:bbb88c44f805
+  elsif @projects.key?(project)
-:56a38a9f6204
+    @projects[project].is_public?
-:bbb88c44f805
+  else
     pobj = Project.find_by_identifier(project)
     if pobj
       @projects[project] = pobj
-:56a38a9f6204
+      pobj.is_public?
-:bbb88c44f805
+    else
-:56a38a9f6204
+      print "Project not found: ", project, "\n"
-:bbb88c44f805
+      false
     end
   end
 end
-:9b4919de5317
+def print_stats(h)
   h.keys.sort { |a,b| h[b] <=> h[a] }.each do |p|
-:6edb748be064
+    if h[p] > 0
-:a97e573d7f87
+      print h[p], " ", @projects[p].name, " [", p, "]\n"
-:6edb748be064
+    end
-:9b4919de5317
+  end
 end
-:56a38a9f6204
+STDIN.each do |line|
-:198f764e734c
+            Chris
   record = parser.parse(line)
   # most annoyingly, the parser can't handle the comma-separated list
   # in X-Forwarded-For where it has more than one element. If it has
-:a97e573d7f87
+  # failed, remove any IP addresses or the word "unknown" with
   # trailing commas and try again
-:198f764e734c
+  if not record
-:a97e573d7f87
+    filtered = line.gsub(/(unknown|([0-9]+\.){3}[0-9]+),\s*/, "")
-:198f764e734c
+    record = parser.parse(filtered)
   end
   # discard, but count, unparseable lines
   if not record
-:56a38a9f6204
+    print "Line not parseable: ", line, "\n"
-:198f764e734c
+    unparseable += 1
     next
   end
   # discard everything that isn't a 200 OK response
   next if record["%>s"] != "200"
   # discard anything apparently requested by a crawler
   next if record["%{User-Agent}i"] =~ /(bot|slurp|crawler|spider|Redmine)\b/i
   # pull out request e.g. GET / HTTP/1.0
   request = record["%r"]
   # split into method, path, protocol
   if not request =~ /^[^\s]+ ([^\s]+) [^\s]+$/
-:56a38a9f6204
+    print "Line not parseable (bad method, path, protocol): ", line, "\n"
-:198f764e734c
+    unparseable += 1
     next
   end
   # get the path e.g. /projects/weevilmatic and split on /
   path = $~[1]
   components = path.split("/")
   # should have at least two elements unless path is "/"; first should
   # be empty (begins with /)
   if path != "/" and (components.size < 2 or components[0] != "")
-:56a38a9f6204
+    print "Line not parseable (degenerate path): ", line, "\n"
-:198f764e734c
+    unparseable += 1
     next
   end
   if components[1] == "hg"
     # path is /hg/project?something or /hg/project/something
     project = components[2].split("?")[0]
-:56a38a9f6204
+    if not is_public_project?(project)
-:bbb88c44f805
+      next
     end
-:198f764e734c
+            Chris
     if components[2] =~ /&roots=00*$/
       clones[project] += 1
     elsif components[2] =~ /cmd=capabilities/
       pulls[project] += 1
-:bbb88c44f805
+    elsif components[2] =~ /cmd=unbundle/
       pushes[project] += 1
-:198f764e734c
+    elsif components[3] == "archive"
       zips[project] += 1
     end
   elsif components[1] == "projects"
     # path is /projects/project or /projects/project/something
     project = components[2]
-:56a38a9f6204
+    project = project.split("?")[0] if project
     if not is_public_project?(project)
-:bbb88c44f805
+      next
-:198f764e734c
+    end
-:bbb88c44f805
+    hits[project] += 1
-:198f764e734c
+  end
   parseable += 1
 end
 # Each clone is also a pull; deduct it from the pulls hash, because we
 # want that to contain only non-clone pulls
 clones.keys.each do |project|
   pulls[project] -= 1
 end
-:6edb748be064
+print parseable, " parseable\n"
 print unparseable, " unparseable\n"
-:9b4919de5317
+print "\nMercurial clones:\n"
 print_stats clones
 print "\nMercurial pulls (excluding clones):\n"
 print_stats pulls
 print "\nMercurial pushes:\n"
 print_stats pushes
 print "\nMercurial archive (zip file) downloads:\n"
 print_stats zips
-:6edb748be064
+print "\nProject page hits (excluding crawlers):\n"
-:9b4919de5317
+print_stats hits
-:198f764e734c
+            Chris
-:e2a3230f61fa
+            Chris
 # Print out an authormap file for hg-to-git conversion using
 # hg-fast-export
+#
 # Invoke with the project identifier as argument, e.g.
+#
 # ./script/rails runner -e production extra/soundsoftware/get-repo-authormap.rb soundsoftware-site
-:e55cbb9ba8bf
+proj_ident = ARGV.last
-:e2a3230f61fa
+proj = Project.find_by_identifier(proj_ident)
 repo = Repository.where(:project_id => proj.id).first
 csets = Changeset.where(:repository_id => repo.id)
 committers = csets.map do |c| c.committer end.sort.uniq
 committers.each do |c|
-:e55cbb9ba8bf
+  if not c =~ /[^<]+<.*@.*>/ then
     u = repo.find_committer_user c
     print "#{c}=#{u.name} <#{u.mail}>\n" unless u.nil?
   end
-:e2a3230f61fa
+end
-:6bd8364eafae
+            luis
-:b554eb79ec7b
+# Log user and project information
+#
 # Invoke with e.g.
+#
 # ./script/rails runner -e production extra/soundsoftware/get-statistics.rb
-:6bd8364eafae
+            luis
-:02a05da0bedc
+projectStats =  {
         :all => Project.active.all.count,
         :private => Project.active.find(:all, :conditions => {:is_public => false}).count,
         :top_level => Project.active.find(:all, :conditions => {:parent_id => nil}).count,
         :top_level_and_private => Project.active.find(:all, :conditions => {:is_public => false, :parent_id => nil}).count
+      }
-:6bd8364eafae
+            luis
-:b554eb79ec7b
+userStats = {:all => User.active.all.count}
-:f6ede18f3e6e
+            Chris
-:b554eb79ec7b
+stats = {:date => Date.today, :projects => projectStats, :users => userStats}.to_json
-:f6ede18f3e6e
+            Chris
-:b554eb79ec7b
+print "#{stats}\n"
-:f6ede18f3e6e
+            Chris
-:47ae83ce8db8
+<div style="clear: both; float: right"><small><i>Produced by mtree2html by Hartmut Pohlheim</i></small></div>
 # configuration file for generation of html-docu from m-files
+#
 # Author:   Hartmut Pohlheim
 # History:  05.11.2000  file created (parameters for mtree2html2001)
+#
 # The following options/variables must be changed/adapted:
 #   dirmfiles
 #   dirhtml
 #   csslink
 #   texttitleframelayout
 #   texttitlefiles
+#
 # The following options/variables should be adapted:
 #   authorfile
 #   filenametopframe
 #   codeheadmeta
 #========================================================================
 # Variables (possible keywords: set)
 # to use the built-in settings, comment the line using # in first column
 #========================================================================
 #------------------------------------------------------------------------
 # dirmfiles: name of directory containing Matlab m-files
 # dirhtml: name of directory to place the html-files into
 # exthtml: extension used for the html files (.html or .htm)
 #          don't forget the point in front of the extension
 #------------------------------------------------------------------------
 set dirmfiles = .
 set dirhtml = doc-output
 set exthtml = .html
 #------------------------------------------------------------------------
 # authorfile:   name of file containing info about author (in html)
 #               if defined, this text is included at the bottom of the
 #               html files
 #------------------------------------------------------------------------
-:675de8e6becf
+set authorfile = matlab-docs-credit.html
-:47ae83ce8db8
+            Chris
 #------------------------------------------------------------------------
 # csslink:   text for linking to css file (style sheets)
 #            the text defined here is directly included into the head
 #            of the html file
 #------------------------------------------------------------------------
-:675de8e6becf
+#set csslink = <link rel=stylesheet type="text/css" href="CSSFILENAME.css" />
-:47ae83ce8db8
+            Chris
 #------------------------------------------------------------------------
 # links2filescase: this is a bit difficult
 #                  Matlab is case sensitive on UNIX, but case insensitive
 #                  on Windows. Under UNIX Matlab function calls work
 #                  only, when the case of file name and function call are
 #                  identical, under Windows you can do what you want.
 #                  This scripts help you, to keep an exact case in your
 #                  project.
 #          exact - internal links are only generated, when case of file
 #                  name and in source code are identical
 #            all - case doesn't matter
 #     exactupper - same as exact, additionally links are also vreated to
 #                  all upper case function names in source code (often
 #                  used by Mathworks)
 #      exactvery - same as exact, additionally info about not matching
 #                  case is written to screen (stdout), this can be very
 #                  helpful in cleaning up the case in a project
 #------------------------------------------------------------------------
 set links2filescase = all
 #------------------------------------------------------------------------
 # texttitleframelayout:    text of title for frame layout file (whole docu)
 #------------------------------------------------------------------------
-:0bc92382a86b
+set texttitleframelayout = MATLAB Function Documentation
-:47ae83ce8db8
+            Chris
 #------------------------------------------------------------------------
 # texttitle/headerindexalldirs: text of title and header for directory index
 #------------------------------------------------------------------------
 set texttitleindexalldirs = Index of Directories
 set textheaderindexalldirs = Index of Directories
 #------------------------------------------------------------------------
 # texttitle/headerindex:    text of title and header for index file
 #------------------------------------------------------------------------
 set texttitleindex = A-Z Index of Functions
 set textheaderindex = A-Z Index of Functions
 #------------------------------------------------------------------------
 # texttitle/headerfiles:    text of title and header for files
 #                           name of file will be added at the end
 #------------------------------------------------------------------------
-:0bc92382a86b
+set texttitlefiles = Function
-:47ae83ce8db8
+set textheaderfiles = Documentation of
 #------------------------------------------------------------------------
 # frames: whether to use frames in layout (yes or no)
 #------------------------------------------------------------------------
 set frames = no
 #------------------------------------------------------------------------
 # filenametopframe: name of file including frame layout (highest level file)
 # [default: index]
 #------------------------------------------------------------------------
 set filenametopframe = index
 #------------------------------------------------------------------------
 # textjumpindexglobal: text displayed for jump to index of all files
 #                      (global)
 # textjumpindexlocal:  text displayed for jump to index of files in actual
 #                      directory (local)
 #------------------------------------------------------------------------
-:0bc92382a86b
+set textjumpindexglobal = <b>Index of</b> all files:
 set textjumpindexlocal = this subdirectory only:
-:47ae83ce8db8
+            Chris
 #------------------------------------------------------------------------
 # includesource: include source of m-files in documentation [YES|no]
 #------------------------------------------------------------------------
 set includesource = yes
 #------------------------------------------------------------------------
 # usecontentsm: use contents.m files as well for structured
 #               (hopefully) index [YES|no]
 #------------------------------------------------------------------------
 set usecontentsm = no
 #------------------------------------------------------------------------
 # includesource: write/update contents.m files [yes|NO]
 #------------------------------------------------------------------------
 set writecontentsm = no
 #------------------------------------------------------------------------
 # processtree:  parse whole directory tree recursively [YES|no]
 #------------------------------------------------------------------------
 set processtree = yes
 #------------------------------------------------------------------------
 # producetree:  produce tree for html-files in same structure than
 #		          tree of m-files [yes|NO]
 #               if no, all files are saved in the same directory, often
 #               easier for outside linking to files
 #------------------------------------------------------------------------
-:a0f6e994657f
+set producetree = yes
-:47ae83ce8db8
+            Chris
 #------------------------------------------------------------------------
 # codebodyindex/files: HTML-code for adding to BODY tag
 #                      can be used for defining colors and
 #                      backgroundimages of the files
 #                      No longer recommended, use the css file
 #------------------------------------------------------------------------
 set codebodyindex =
 set codebodyfiles =
 #------------------------------------------------------------------------
 # codeheadmeta: HTML-code added in HEAD area, use for supplying META info
 #------------------------------------------------------------------------
 set codeheadmeta =
 #------------------------------------------------------------------------
 # codehr: HTML-code used to define a <HR>, do what you want
 #------------------------------------------------------------------------
-:e7ba81c8dc5a
+set codehr = <hr>
-:47ae83ce8db8
+            Chris
 #------------------------------------------------------------------------
 # codeheader: HTML-code added to <H*> tags, use for centering header text
 #             or changing the colour/size/font of the header text
 #------------------------------------------------------------------------
-:0bc92382a86b
+set codeheader =
-:47ae83ce8db8
+            Chris
 # End of parameter file
-:2dc8163e9150
+@rem = '--*-Perl-*--';
 @rem = '
 @echo off
 perl -w -S %0.bat %1 %2 %3 %4 %5 %6 %7 %8 %9
 goto endofperl
 @rem ';
 # perl -w -S %0.bat "$@"
-:baff1c482d98
+#!/usr/bin/perl
-:2dc8163e9150
+            Chris
 # mtree2html_2000 - produce html files from Matlab m-files.
 #                   use configuration file for flexibility
 #                   can process tree of directories
+#
 # Copyright (C) 1996-2000 Hartmut Pohlheim.  All rights reserved.
 # includes small parts of m2html from Jeffrey C. Kantor 1995
+#
 # Author:  Hartmut Pohlheim
 # History: 06.03.1996  file created
 #          07.03.1996  first working version
 #          08.03.1996  modularized, help text only once included
 #          11.03.1996  clean up, some functions rwritten
 #          18.04.1996  silent output with writing in one line only
 #                      version 0.20 fixed
 #          14.05.1996  start of adding tree structure, could create tree
 #          15.05.1996  creating of index files for every directory
 #          17.05.1996  first working version except compact A-Z index
 #          20.05.1996  cleanup of actual version, more variables and
 #                      configurable settings
 #          21.05.1996  reading, update and creation of contents.m added
 #          22.05.1996  creation of short index started
 #          28.05.1996  jump letters for short index,
 #                      3 different directory indexes (short/long/contents)
 #          29.05.1996  major cleanup, short and long index created from one function
 #                      links for HTML and Indexes from 1 function,
 #                      version 0.9
 #          30.05.1996  contents.m changed to Contents.m (because unix likes it)
 #                      function definition can be in first line of m file before comments
 #                      version 0.91 fixed
 #          03.06.1996  contents file can be written as wanted, the links will be correct
 #                      cross references in help block of m-file will be found and
 #                      converted, even if the name of the function is written upper case
 #                      version 0.92 fixed
 #          05.06.1996  construction of dependency matrix changed, is able now to process
 #                      even the whole matlab tree (previous version needed to much memory)
 #                      removed warning for contents files in different directories
 #                      version 0.94 fixed
 #          06.06.1996  new link name matrices for ConstructHTMLFile created,
 #                      everything is done in ConstructDependencyMatrix,
 #                      both dependencies (calls and called) and matrix
 #                      with all mentioned names in this m-file, thus, much
 #                      less scanning in html construction
 #                      script is now (nearly) linear scalable, thus, matlab-toolbox
 #                      tree takes less than 1 hour on a Pentium120, with source
 #                      version 0.96 fixed
 #          10.06.1996  order of creation changed, first all indexes (includes
 #                      update/creation of contents.m) and then ConstructDepency
 #                      thus, AutoAdd section will be linked as well
 #                      excludenames extended, some more common word function names added
 #                      version 0.97 fixed
 #          17.02.1998  writecontentsm as command line parameter added
 #                      error of file not found will even appear when silent
 #                      version 1.02
 #          21.05.2000  mark comments in source code specially (no fully correct,
 #                      can't handle % in strings)
 #                      version 1.11
 #          05.11.2000  link also to upper and mixed case m-files
 #                      searching for .m files now really works (doesn't find grep.com any longer)
 #                      file renamed to mtree2html2001
 #                      generated html code now all lower case
 #                      inclusion of meta-description and meta-keywords in html files
 #                      HTML4 compliance done (should be strict HTML4.0, quite near XHTML)
 #                      version 1.23
+#
-:47ae83ce8db8
+#	   29.03.2011  (Chris Cannam) add frames option.
-:2dc8163e9150
+            Chris
 $VERSION  = '1.23';
 ($PROGRAM = $0) =~ s@.*/@@; $PROGRAM = "\U$PROGRAM\E";
-:e7ba81c8dc5a
+$debug = 1;
-:2dc8163e9150
+            Chris
 #------------------------------------------------------------------------
 # Define platform specific things
 #------------------------------------------------------------------------
 # suffix for files to search is defined twice
 # the first ($suffix) is for string creation and contains the . as well
 # the second ($suffixforsearch) is for regular expression, handling of . is quite special
 $suffix = ".m";
 $suffixforsearch = "m";
 # the directory separator
 $dirsep = "/";
 # what is the current directory
 $diract = ".";
 #------------------------------------------------------------------------
-:baff1c482d98
+#  Define all variables and their standard settings
-:2dc8163e9150
+#  documentation of variables is contained in accompanying rc file
 #------------------------------------------------------------------------
 %var =
+(
    'authorfile',                '',
    'codebodyfiles',             '',
    'codebodyindex',             '',
    'codeheadmeta',              '<meta name="author of conversion perl script" content="Hartmut Pohlheim" />',
    'codehr',                    '<hr size="3" noshade="noshade" />',
    'codeheader',                '',
-:47ae83ce8db8
+   'configfile',                'matlab-docs.conf',
-:2dc8163e9150
+   'csslink',                   '',
    'dirmfiles',                 $diract,
    'dirhtml',                   $diract,
    'exthtml',                   '.html',
-:baff1c482d98
+   'frames',                    'yes',
-:2dc8163e9150
+   'filenametopframe',          'index',
    'filenameindexlongglobal',   'indexlg',
    'filenameindexlonglocal',    'indexll',
    'filenameindexshortglobal',  'indexsg',
    'filenameindexshortlocal',   'indexsl',
    'filenameextensionframe',    'f',
    'filenameextensionindex',    'i',
    'filenameextensionjump',     'j',
    'filenamedirshort',          'dirtops',
    'filenamedirlong',           'dirtopl',
    'filenamedircontents',       'dirtopc',
    'includesource',             'yes',
    'links2filescase',           'all',
    'processtree',               'yes',
    'producetree',               'yes',
    'textjumpindexlocal',        'Local Index',
    'textjumpindexglobal',       'Global Index',
    'texttitleframelayout',      'Documentation of Matlab Files',
    'texttitleindexalldirs',     'Index of Directories',
    'textheaderindexalldirs',    'Index of Directories',
    'texttitleindex',            '',
    'textheaderindex',           '',
    'texttitlefiles',            'Documentation of ',
    'textheaderfiles',           'Documentation of ',
    'usecontentsm',              'yes',
    'writecontentsm',            'no'
 );
 # define all m-file names, that should be excluded from linking
 # however, files will still be converted
 @excludenames = ( 'all','ans','any','are',
                   'cs',
                   'demo','dos',
                   'echo','edit','else','elseif','end','exist',
                   'flag','for','function',
                   'global',
                   'help',
                   'i','if','inf','info',
                   'j',
                   'more',
                   'null',
                   'return',
                   'script','strings',
                   'what','which','while','who','whos','why',
                 );
 # Text for inclusion in created HTML/Frame files: Doctype and Charset
 $TextDocTypeHTML  = '<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">';
 $TextDocTypeFrame = '<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Frameset//EN" "http://www.w3.org/TR/REC-html40/frameset.dtd">';
 $TextMetaCharset = '<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1" />';
 #------------------------------------------------------------------------
 # Read the command line arguments
 #------------------------------------------------------------------------
 if (@ARGV == 0) {
    &DisplayHelp()  if &CheckFileName($var{'configfile'}, 'configuration file');
+}
 # Print provided command line arguments on screen
 foreach (@ARGV) { print "   $_\n      "; }
 # Get the options
 use Getopt::Long;
 @options = ('help|h', 'todo|t', 'version|v',
             'authorfile|a=s', 'configfile|c=s', 'dirhtml|html|d=s',
             'dirmfiles|mfiles|m=s', 'includesource|i=s',
             'processtree|r=s', 'producetree|p=s',
             'silent|quiet|q', 'writecontentsm|w=s');
 &GetOptions(@options) || die "use -h switch to display help statement\n";
 # Display help or todo list, when requested
 &DisplayHelp()                         if $opt_help;
 &DisplayTodo()                         if $opt_todo;
 die "$PROGRAM v$VERSION\n"             if $opt_version;
 $exit_status = 0;
 #------------------------------------------------------------------------
 # Read the config file
 #------------------------------------------------------------------------
 $var{'configfile'} = $opt_configfile         if $opt_configfile;
 &GetConfigFile($var{'configfile'});
 #------------------------------------------------------------------------
 # Process/Check the command line otions
 #------------------------------------------------------------------------
 $var{'dirhtml'}   = $opt_dirhtml              if $opt_dirhtml;
 if (!(substr($var{'dirhtml'}, -1, 1) eq $dirsep)) { $var{'dirhtml'} = $var{'dirhtml'}.$dirsep; }
 $var{'dirmfiles'} = $opt_dirmfiles            if $opt_dirmfiles;
 if (!(substr($var{'dirmfiles'}, -1, 1) eq $dirsep)) { $var{'dirmfiles'} = $var{'dirmfiles'}.$dirsep; }
 $var{'authorfile'} = $opt_author              if $opt_author;
 $var{'includesource'} = $opt_includesource    if $opt_includesource;
 if ($var{'includesource'} ne 'no') { $var{'includesource'} = 'yes'; }
 $var{'processtree'} = $opt_processtree        if $opt_processtree;
 if ($var{'processtree'} ne 'no') { $var{'processtree'} = 'yes'; }
 $var{'producetree'} = $opt_producetree        if $opt_producetree;
 if ($var{'producetree'} ne 'no') { $var{'producetree'} = 'yes'; }
 if ($var{'processtree'} eq 'no') { $var{'producetree'} = 'no'; }
-:baff1c482d98
+if ($var{'frames'} ne 'no') { $var{'frames'} = 'yes'; }
-:2dc8163e9150
+# if (($var{'processtree'} eq 'yes') && ($var{'producetree'} eq 'no')) { $var{'usecontentsm'} = 'no'; }
 $var{'writecontentsm'} = $opt_writecontentsm  if $opt_writecontentsm;
 #------------------------------------------------------------------------
 # Do the real stuff
 #------------------------------------------------------------------------
 # Print variables on screen, when not silent
 &ListVariables                          if !$opt_silent;
 # Check the author file
 if ($var{'authorfile'} ne '') {
-:675de8e6becf
+    if (!($var{'authorfile'} =~ m,^/,)) {
 	# relative path: treat as relative to config file
 	my $cfd = $var{'configfile'};
 	$cfd =~ s,/[^/]*$,/,;
 	$cfd =~ s,^[^/]*$,.,;
 	$var{'authorfile'} = "$cfd/" . $var{'authorfile'};
+    }
     if (&CheckFileName($var{'authorfile'}, 'author file')) {
 	$var{'authorfile'} = '';
 	if (!$opt_silent) { print "   Proceeding without author information!\n"; }
+    }
-:2dc8163e9150
+            Chris
 # Call the function doing all the real work
 &ConstructNameMatrix;
 &ConstructDependencyMatrix;
 &ConstructAllIndexFiles;
 &ConstructHTMLFiles;
 exit $exit_status;
 #------------------------------------------------------------------------
 # Construct list of all mfile names and initialize various data arrays.
 #------------------------------------------------------------------------
 sub ConstructNameMatrix
+{
    local(*MFILE);
    local($file, $dirname);
    local(@newdirectories);
    local(%localnames);
    $RecDeep = 0;
    &ParseTreeReadFiles($var{'dirmfiles'}, $RecDeep);
    foreach $dirname (@directories) {
       if ($dirnumbermfiles{$dirname} > 0) {
          push(@newdirectories, $dirname);
          if (! defined($contentsname{$dirname})) {
             $contentsname{$dirname} = 'Contents';
             if (($var{'writecontentsm'} eq 'no') && ($var{'usecontentsm'} eq 'yes')) {
                print "\r ParseTree - for directory  $dirname  no contents file found!\n";
                print   "             create one or enable writing of contents file (writecontentsm = yes)!\n";
+            }
+         }
+      }
+   }
    @alldirectories = @directories;
    @directories = @newdirectories;
    foreach $dirname (@directories) {
       if ($debug > 0) { print "Dir: $dirname \t\t $dirnumbermfiles{$dirname} \t$contentsname{$dirname}\n"; }
+   }
    @names = sort(keys %mfile);
    # check, if name of directory is identical to name of file
    @dirsinglenames = values(%dirnamesingle);
    grep($localnames{$_}++, @dirsinglenames);
    @dirandfilename = grep($localnames{$_}, @names);
    if (@dirandfilename) {
       print "\r   Name clash between directory and file name: @dirandfilename\n";
       print   "      These files will be excluded from linking!\n";
       push(@excludenames, @dirandfilename);
+   }
    # construct names matrix for help text linking
    #    exclude some common words (and at the same time m-functions) from linking in help text
    grep($localnames{$_}++, @excludenames);
    @linknames = grep(!$localnames{$_}, @names);
    if ($debug > 2) { print "linknames (names of found m-files):\n    @linknames\n"; }
+}
 #------------------------------------------------------------------------
 # Parse tree and collect all Files
 #------------------------------------------------------------------------
 sub ParseTreeReadFiles
+{
    local($dirname, $localRecDeep) = @_;
    local($file, $name, $filewosuffix);
    local($dirhtmlname, $dirmode);
    local($relpath, $relpathtoindex, $replacevardir);
    local(*CHECKDIR, *AKTDIR);
    local(@ALLEFILES);
    opendir(AKTDIR, $dirname) || die "ParseTree - Can't open directory $dirname: $!";
    if ($debug > 1) { print "\nDirectory: $dirname\n"; }
    # create relative path
    $_ = $dirname; $replacevardir = $var{'dirmfiles'};
    s/$replacevardir//; $relpath = $_;
    s/[^\/]+/../g; $relpathtoindex = $_;
    # producetree no
    if ($var{'producetree'} eq 'no') { $relpath = ''; $relpathtoindex = ''; }
    # names of directories (top-level and below top-level m-file-directory)
    push(@directories, $dirname);
    $dirnumbermfiles{$dirname} = 0;    # set number of m-files for this dir to zero
    # relative path from top-level directory, depends on directory name
    $dirnamerelpath{$dirname} = $relpath;
    # relative path from actual directory to top-level directory, depends on directory name
    $dirnamerelpathtoindex{$dirname} = $relpathtoindex;
    # recursion level for directory, depends on directory name
    $dirnamerecdeep{$dirname} = $localRecDeep;
    # only the name of the directory, without path
    $rindexprint = rindex($dirname, $dirsep, length($dirname)-2);
    $rindsub = substr($dirname, $rindexprint+1, length($dirname)-$rindexprint-2);
    $dirnamesingle{$dirname} = $rindsub;
    # create name of html-directories
    $_ = $dirname;
    s/$var{'dirmfiles'}/$var{'dirhtml'}/;
    $dirhtmlname = $_;
    if ($var{'producetree'} eq 'no') { $dirhtmlname = $var{'dirhtml'}; }
    # try to open html directory, if error, then create directory,
    # use same mode as for corresponding m-file directory
    opendir(CHECKDIR,"$dirhtmlname") || do {
       $dirmode = (stat($dirname))[2]; # print "$dirmode\n";
       mkdir("$dirhtmlname", $dirmode) || die ("Cannot create directory $dirhtmlname: $! !");
    };
    closedir(CHECKDIR);
    # read everything from this directory and process them
    @ALLEFILES = readdir(AKTDIR);
    foreach $file (@ALLEFILES) {
       # exclude . and .. directories
       next if $file eq '.';  next if $file eq '..';
       # test for existense of entry (redundant, used for debugging)
       if (-e $dirname.$file) {
          # if it's a directory, call this function recursively
          if (-d $dirname.$file) {
             if ($var{'processtree'} eq 'yes') {
                &ParseTreeReadFiles($dirname.$file.$dirsep, $localRecDeep+1);
+            }
+         }
          # if it's a file - test for m-file, save name and create some arrays
          elsif (-f $dirname.$file) {
             if ($file =~ /\.$suffixforsearch$/i) {
                # Remove the file suffix to establish the matlab identifiers
                $filewosuffix = $file;
                $filewosuffix =~ s/\.$suffixforsearch$//i;
                # $filename = $name;
                # Contents file in unix must start with a capital letter (Contents.m)
                # ensure, that m-file name is lower case, except the contents file
                if (! ($filewosuffix =~ /^contents$/i)) {
-:dad587ecb8d0
+		   # if ($var{'links2filescase'}  eq 'low') { $filewosuffix = "\L$filewosuffix\E"; }
-:2dc8163e9150
+                  $filewosuffixlow = "\L$filewosuffix\E";
+               }
                else { $contentsname{$dirname} = $filewosuffix; }
                # internal handle name is always lower case
                $name     = $filewosuffixlow;
                # file name is not lower case
                $filename = $filewosuffix;
                # if don't use C|contents.m, then forget all C|contents.m
                if ($var{'usecontentsm'} eq 'no') { if ($name =~ /contents/i) { next; } }
                # if m-file with this name already exists, use directory and name for name
                # only the first occurence of name will be used for links
                if (defined $mfile{$name}) {
                   if (! ($name =~ /^contents$/i) ) {
                      print "\r ParseTree - Name conflict:  $name in $dirname already exists: $mfile{$name} !\n";
                      print   "             $mfile{$name}  will be used for links!\n";
+                  }
                   $name = $dirname.$name;
+               }
                # mfile name with path
                $mfile{$name} = $dirname.$file;
                # mfile name (without path)
                $mfilename{$name} = $filename;
                # mfile directory
                $mfiledir{$name} = $dirname;
                # html file name and full path, special extension of Contents files
                if ($name =~ /contents/i) { $extrahtmlfilename = $dirnamesingle{$dirname}; }
                else { $extrahtmlfilename = ''; }
                $hfile{$name} = $dirhtmlname.$mfilename{$name}.$extrahtmlfilename.$var{'exthtml'};
                # save relative html path
                # if ($var{'producetree'} eq 'yes') {
                $hfilerelpath{$name} = $relpath;
                # } else { # if no tree to produce, relative path is empty
                #    $hfilerelpath{$name} = '';
                # }
                # create relative path from html file to directory with global index file
                $hfileindexpath{$name} = $relpathtoindex;
                # Function declaration, if one exists, set default to script
                $synopsis{$name} = "";
                $mtype{$name} = "script";
                # First comment line
                $apropos{$name} = "";
                # count number of m-files in directories
                $dirnumbermfiles{$dirname}++;
                if ($debug > 1) {
                   if ($opt_silent) { print "\r"; }
                   print "   ParseTree: $name \t\t $mfile{$name} \t\t $hfile{$name}\t\t";
                   if (!$opt_silent) { print "\n"; }
+               }
+            }
+         }
          else {
             print "Unknown type of file in $dirname: $file\n";
+         }
+      }
       else { print "Error: Not existing file in $dirname: $file\n"; }
+   }
    closedir(AKTDIR)
+}
 #------------------------------------------------------------------------
 # Construct Dependency matrix
 #    $dep{$x,$y} > 0 if $x includes a reference to $y.
 #------------------------------------------------------------------------
 sub ConstructDependencyMatrix
+{
    &ConstructDependencyMatrixReadFiles('all');
    &ConstructDependencyMatrixReally;
+}
 #------------------------------------------------------------------------
 # Construct Dependency matrix
 #    $dep{$x,$y} > 0 if $x includes a reference to $y.
 #------------------------------------------------------------------------
 sub ConstructDependencyMatrixReadFiles
+{
    local($whatstring) = @_;
    local(*MFILE);
    local($name, $inames);
    local(%symbolsdep, %symbolsall);
    # Initialize as all zeros.
    # foreach $name (@names) { grep($dep{$name,$_}=0,@names); if ($debug > 0) { print "\r   DepMatrix anlegen: $name\t$#names\t"; } }
    # Compute the dependency matrix
    $inames = -1;
    foreach $name (@names) {
       # Read each file and tabulate the distinct alphanumeric identifiers in
       # an array of symbols. Also scan for:
       #   synopsis: The function declaration line
       #   apropos:  The first line of the help text
       # look for whatstring, if all: process every file, if contents: process only contents files
       if ($whatstring eq 'contents') { if (! ($name =~ /contents$/i) ) { next; } }
       elsif ($whatstring eq 'all') { }    # do nothing
       else { print "\r   ConstructDependency: Unknown parameter whatstring: $whatstring \n"; }
       undef %symbolsall; undef %symbolsdep;
       open(MFILE,"<$mfile{$name}") || die("Can't open $mfile{$name}: $!\n");
       while (<MFILE>) {
          chop;
          # Split on nonalphanumerics, then look for all words, used for links later
          # this one for all references
          @wordsall = grep(/[a-zA-Z]\w*/, split('\W',$_));
          # set all words to lower case for link checking
          undef @wordsall2;
          # do case conversion not, case checking is done later
          foreach (@wordsall) { push(@wordsall2, "\L$_\E"); }
          # @wordsall2 = @wordsall;
          grep($symbolsall{$_}++, @wordsall2);
          # Store first comment line, skip all others.
          if (/^\s*%/) {
             if (!$apropos{$name}) {
                s/^\s*%\s*//;   # remove % and leading white spaces on line
                $_ = &SubstituteHTMLEntities($_);
                $apropos{$name} = $_;
+            }
             next;
+         }
          # If it's the function declaration line, then store it and skip
          # but only, when first function definition (multiple function lines when private subfunctions in file
          if ($synopsis{$name} eq '') {
             if (/^\s*function/) {
                s/^\s*function\s*//;
                $synopsis{$name} = $_;
                $mtype{$name} = "function";
                next;
+            }
+         }
          # Split off any trailing comments
          if ($_ ne '') {
             # this one for references in program code only
             # when syntax parsing, here is a working place
             ($statement) = split('%',$_,1);
             @wordsdep = grep(/[a-zA-Z]\w*/,split('\W',$statement));
             # do case conversion not, case checking is done later
             undef @wordsdep2;
             foreach (@wordsdep) { push(@wordsdep2, "\L$_\E"); }
             grep($symbolsdep{$_}++, @wordsdep2);
+         }
+      }
       close MFILE;
       # compute intersection between %symbolsall and @linknames
       delete($symbolsall{$name});
       # foreach $localsumall ($symbolsall) {
       #    $localsumall = "\L$localsumall\E";
       # }
       @{'all'.$name} = grep($symbolsall{$_}, @linknames);
       # compute intersection between %symbolsdep and @linknames
       delete($symbolsdep{$name});
       @{'depcalls'.$name} = grep($symbolsdep{$_}, @linknames);
       $inames++; print "\r   DepCallsMatrix: $inames/$#names\t $name\t";
       if ($debug > 2) { print "\n      depnames: @{'depcalls'.$name}\n      all: @{'all'.$name}\n"; }
+   }
+}
 #------------------------------------------------------------------------
 # Construct Dependency matrix
 #    $dep{$x,$y} > 0 if $x includes a reference to $y.
 #------------------------------------------------------------------------
 sub ConstructDependencyMatrixReally
+{
    local($inames, $name);
    $inames = -1;
    foreach $name (@names) { undef %{'depint'.$name}; }
    foreach $name (@names) {
       grep(${'depint'.$_}{$name}++, @{'depcalls'.$name});
       $inames++; print "\r   DepCalledMatrix1: $inames/$#names\t $name\t";
+   }
    $inames = -1;
    foreach $name (@names) {
       # compute intersection between %depint.name{$_} and @linknames
       if (defined (%{'depint'.$name})) { @{'depcalled'.$name} = grep(${'depint'.$name}{$_}, @linknames); }
       $inames++; print "\r   DepCalledMatrix2: $inames/$#names\t $name\t";
       if ($debug > 2) { print "\n      depcalled: @{'depcalled'.$name}\n"; }
+   }
+}
 #========================================================================
 # Construct all index files
 #========================================================================
 sub ConstructAllIndexFiles
+{
    local(@localnames);
    local($ActDir);
    local($name);
    # define variables and names for frame target
    $GlobalNameFrameMainLeft = 'Cont_Main';
    $GlobalNameFrameMainRight = 'Cont_Lower';
    $GlobalNameFrameAZIndexsmall = 'IndexAZindex';
    $GlobalNameFrameAZIndexjump = 'IndexAZjump';
    $indexcreated = 0;
    &ConstructHighestIndexFile;
    $indexcreated++;
    # if ($var{'producetree'} eq 'yes') {
       # moved next 2 lines out of if for producetree no
       # &ConstructHighestIndexFile;
       # $indexcreated++;
       foreach $ActDir (@directories) {
          undef @localnames;
          foreach $name (@names) {
             local($pathsubstr) = substr($mfile{$name}, 0, rindex($mfile{$name}, "/")+1);
             if ($ActDir eq $pathsubstr) {
                if ($debug > 1) { print "IndexFile: $pathsubstr    ActDir: $ActDir   Hfilerelpath: $hfilerelpath{$name}\n"; }
                push(@localnames, $name);
+            }
+         }
          if ($debug > 2) { print "localnames: @localnames\n"; }
          # create contents file and short|long index of files in local directory
          &ConstructContentsmFile($ActDir, @localnames);
          &ConstructAZIndexFile($ActDir, 'short', 'local', @localnames);
          &ConstructAZIndexFile($ActDir, 'long', 'local', @localnames);
          $indexcreated+=2;
+      }
    # } else {
    #    &ConstructContentsmFile($var{'dirmfiles'}, @names);
    # }
    # create short|long index of files in all directory
    &ConstructAZIndexFile($var{'dirmfiles'}, 'short', 'global', @names);
    &ConstructAZIndexFile($var{'dirmfiles'}, 'long', 'global', @names);
    $indexcreated+=2;
    # if contents.m were created or updated, the dependency matrices should
    # be updated as well
    if ($var{'writecontentsm'} eq 'yes') { &ConstructDependencyMatrixReadFiles('contents');; }
+}
 #========================================================================
 # Construct the highest level index file
 #========================================================================
 sub ConstructHighestIndexFile
+{
    local(*IFILE);
    local($indexfile, $filename);
    # Build the frame layout file, this files includes the layout of the frames
    # Build the frame layout file name (highest one)
    $indexfile = $var{'dirhtml'}.$var{'filenametopframe'}.$var{'exthtml'};
-:baff1c482d98
+   if ($var{'frames'} eq 'yes') {
-:2dc8163e9150
+            Chris
-:baff1c482d98
+       open(IFILE,">$indexfile") || die("Cannot open frame layout file $indexfile\n");
-:2dc8163e9150
+            Chris
-:baff1c482d98
+       # Write the header of frame file
        print IFILE "$TextDocTypeFrame\n<html>\n<head>\n$var{'codeheadmeta'}\n$TextMetaCharset\n";
        print IFILE "   <title>$var{'texttitleframelayout'}</title>\n";
        print IFILE "</head>\n";
-:2dc8163e9150
+            Chris
-:baff1c482d98
+       # definition of 2 frames, left the tree of directories,
        # right the index of that directory or the docu of a file
        print IFILE "<frameset  cols=\"25%,75%\">\n";
        print IFILE "   <frame src=\"$var{'filenamedirshort'}$var{'exthtml'}\" name=\"$GlobalNameFrameMainLeft\" />\n";
        print IFILE "   <frame src=\"$var{'filenameindexshortglobal'}$var{'filenameextensionframe'}$var{'exthtml'}\" name=\"$GlobalNameFrameMainRight\" />\n";   print IFILE "</frameset>\n";
-:2dc8163e9150
+            Chris
-:baff1c482d98
+       print IFILE "</html>\n";
        close(IFILE);
        if ($opt_silent) { print "\r"; }
        print "   Frame layout file created: $indexfile\t";
        if (!$opt_silent) { print "\n"; }
+   }
-:2dc8163e9150
+            Chris
    for($irun=0; $irun <= 2; $irun++) {
       # Build the top directory index file, these files include the directory tree
       # Build the directory tree index file name
       # Create no directory file for contents, when no contents to use
       if (($irun == 2) && ($var{'usecontentsm'} eq 'no')) { next; }
       # Assign the correct index file name
       if ($irun == 0) { $filename = $var{'filenamedirshort'}; }
       elsif ($irun == 1) { $filename = $var{'filenamedirlong'}; }
       elsif ($irun == 2) { $filename = $var{'filenamedircontents'}; }
       $indexfile = $var{'dirhtml'}.$filename.$var{'exthtml'};
       open(IFILE,">$indexfile") || die("Cannot open directory tree index file $indexfile\n");
       # Write header of HTML file
       print IFILE "$TextDocTypeHTML\n<html>\n<head>\n$var{'codeheadmeta'}\n$TextMetaCharset\n$var{'csslink'}\n";
       if ($var{'texttitleindexalldirs'} eq '') {
          print IFILE "<title>Index of Directories of $var{'dirmfiles'}</title>\n";
       } else {
          print IFILE "<title>$var{'texttitleindexalldirs'}</title>\n";
+      }
-:baff1c482d98
+            Chris
       if ($var{'frames'} eq 'yes') {
 	  print IFILE "<base target=\"$GlobalNameFrameMainRight\" />\n";
+      }
-:2dc8163e9150
+      print IFILE "</head>\n";
       print IFILE "<body $var{'codebodyindex'}>\n";
-:675de8e6becf
+      print IFILE "<div id=\"matlabdoc\">\n";
-:2dc8163e9150
+      if ($var{'textheaderindexalldirs'} eq '') {
          print IFILE "<h1 $var{'codeheader'}>Index of Directories of <em>$var{'dirmfiles'}</em></h1>\n";
       } else {
          print IFILE "<h1 $var{'codeheader'}>$var{'textheaderindexalldirs'}</h1>\n";
+      }
-:0bc92382a86b
+      print IFILE "<p>\n";
-:baff1c482d98
+            Chris
       if ($var{'frames'} eq 'yes') {
 	  if ($irun == 0) { print IFILE "<strong>short</strong>\n"; }
 	  else { print IFILE "<a href=\"$var{'filenamedirshort'}$var{'exthtml'}\" target=\"$GlobalNameFrameMainLeft\">short</a>\n"; }
 	  if ($irun == 1) { print IFILE " | <strong>long</strong>\n"; }
 	  else { print IFILE " | <a href=\"$var{'filenamedirlong'}$var{'exthtml'}\" target=\"$GlobalNameFrameMainLeft\">long</a>\n"; }
 	  if ($var{'usecontentsm'} eq 'yes') {
 	      if ($irun == 2) { print IFILE " | <strong>contents</strong>\n"; }
 	      else { print IFILE " | <a href=\"$var{'filenamedircontents'}$var{'exthtml'}\" target=\"$GlobalNameFrameMainLeft\">contents</a>\n"; }
+	  }
       } else {
 	  if ($irun == 0) { print IFILE "<strong>short</strong>\n"; }
 	  else { print IFILE "<a href=\"$var{'filenamedirshort'}$var{'exthtml'}\">short</a>\n"; }
 	  if ($irun == 1) { print IFILE " | <strong>long</strong>\n"; }
 	  else { print IFILE " | <a href=\"$var{'filenamedirlong'}$var{'exthtml'}\">long</a>\n"; }
 	  if ($var{'usecontentsm'} eq 'yes') {
 	      if ($irun == 2) { print IFILE " | <strong>contents</strong>\n"; }
 	      else { print IFILE " | <a href=\"$var{'filenamedircontents'}$var{'exthtml'}\">contents</a>\n"; }
+	  }
-:2dc8163e9150
+            Chris
       print IFILE "</p><br />\n\n";
       print IFILE "<ul>\n";
       # go through all directories and create a list entry for each one,
       # depending on recursion level create sublists
       $prevrecdeeplevel = 0;
       foreach $name (@alldirectories) {
          $actrecdeeplevel = $dirnamerecdeep{$name};
          for( ; $prevrecdeeplevel < $actrecdeeplevel; $prevrecdeeplevel++ ) { print IFILE "<ul>\n"; }
          for( ; $prevrecdeeplevel > $actrecdeeplevel; $prevrecdeeplevel-- ) { print IFILE "</ul>\n"; }
          if ($irun == 0) { $indexfilenameused = $var{'filenameindexshortlocal'}.$var{'filenameextensionframe'}; }
          elsif ($irun == 1) { $indexfilenameused = $var{'filenameindexlonglocal'}.$var{'filenameextensionframe'}; }
          elsif ($irun == 2) { $indexfilenameused = $contentsname{$name}; }
          else { die "ConstructHighestIndexFile: Unknown value of irun"; }
          if ($dirnumbermfiles{$name} > 0) {
             # producetree no
             # if ($var{'producetree'} eq 'no') { $dirnamehere = ''; }
             # else { $dirnamehere = '$dirnamerelpath{$name}'; }
             # print IFILE "<LI><A HREF=\"$dirnamehere$indexfilenameused_$dirnamesingle{$name}$var{'exthtml'}\">$dirnamesingle{$name}</A>\n";
             print IFILE "<li><a href=\"$dirnamerelpath{$name}$indexfilenameused$dirnamesingle{$name}$var{'exthtml'}\">$dirnamesingle{$name}</a></li>\n";
          } else {
             # print directories with no m-files inside not
             # print IFILE "<li>$dirnamesingle{$name}</li>\n";
+         }
+      }
       $actrecdeeplevel = 0;
       for( ; $prevrecdeeplevel > $actrecdeeplevel; $prevrecdeeplevel-- ) { print IFILE "</ul>\n"; }
       print IFILE "</ul>\n<br />$var{'codehr'}\n";
       # Include info about author from authorfile
       &WriteFile2Handle($var{'authorfile'}, IFILE);
       print IFILE "<!--navigate-->\n";
       print IFILE "<!--copyright-->\n";
-:675de8e6becf
+      print IFILE "</div>\n</body>\n</html>\n";
-:2dc8163e9150
+            Chris
       close(IFILE);
       if ($opt_silent) { print "\r"; }
       print "   Directory - Indexfile created: $indexfile\t";
       if (!$opt_silent) { print "\n"; }
+   }
+}
 #========================================================================
 # Construct the A-Z index file (global/local and/or short/long)
 #========================================================================
 sub ConstructAZIndexFile
+{
    local($LocalActDir, $LocalShortLong, $LocalGlobalLocal, @localnames) = @_;
    local(*IFILE);
    local($name, $indexfilename, $dirpath);
    local($firstletter, $firstone);
    if ($debug > 2) { print "localnames in AZ small: @localnames\n"; print "     ActDir in A-Z: $LocalActDir\n"; }
    # extract filename of index file from parameters of function
    if ($LocalShortLong eq 'short') {
       if ($LocalGlobalLocal eq 'global') { $indexfilename = $var{'filenameindexshortglobal'}; }
       elsif ($LocalGlobalLocal eq 'local') { $indexfilename = $var{'filenameindexshortlocal'}; }
       else { die "wrong parameter for LocalGlobalLocal in ConstructAZIndexFile: $LocalGlobalLocal."; }
    } elsif ($LocalShortLong eq 'long') {
       if ($LocalGlobalLocal eq 'global') { $indexfilename = $var{'filenameindexlongglobal'}; }
       elsif ($LocalGlobalLocal eq 'local') { $indexfilename = $var{'filenameindexlonglocal'}; }
       else { die "wrong parameter for LocalGlobalLocal in ConstructAZIndexFile: $LocalGlobalLocal."; }
    } else { die "wrong parameter for LocalShortLong in ConstructAZIndexFile: $LocalShortLong."; }
    # producetree no
    # if ($var{'producetree'} eq 'no') { $dirnamehere = ''; }
    # else { $dirnamehere = '$dirnamerelpath{$LocalActDir}'; }
    # Build the index file name
    # handle the global index file case separately (no extra directory name in file)
    #    the local index file name must be extended by the name of the directory
    if ($LocalGlobalLocal eq 'global') { $extradirfilename = ''; }
    else { $extradirfilename = $dirnamesingle{$LocalActDir}; }
    $indexfile = $var{'dirhtml'}.$dirnamerelpath{$LocalActDir}.$indexfilename.$var{'filenameextensionindex'}.$extradirfilename.$var{'exthtml'};
-:baff1c482d98
+            Chris
-:a0f6e994657f
+   if ($LocalShortLong eq 'short' and $extradirfilename eq '' and $var{'frames'} ne 'yes') {
        # With no frames and no subdir path, this must go in the
        # top-level index file instead
-:baff1c482d98
+       $indexfile = $var{'dirhtml'}.$var{'filenametopframe'}.$var{'exthtml'};
+   }
-:2dc8163e9150
+   if ($debug > 2) { print "   indexfilename (a-z small): $indexfile\n"; }
    open(IFILE,">$indexfile") || die("Cannot open index file $indexfile: $!\n");
    # Write the header of HTML file
    print IFILE "$TextDocTypeHTML\n<html>\n<head>\n$var{'codeheadmeta'}\n$TextMetaCharset\n$var{'csslink'}\n";
-:675de8e6becf
+   my $dirToPrint = $LocalActDir;
    $dirToPrint =~ s,^./,,;
-:2dc8163e9150
+   if ($var{'texttitleindex'} eq '') {
-:675de8e6becf
+      print IFILE "<title>Index of Matlab Files in Directory $dirToPrint</title>\n";
-:2dc8163e9150
+   } else {
       if ($LocalGlobalLocal eq 'global') { print IFILE "<title>$var{'texttitleindex'}</title>\n"; }
-:675de8e6becf
+      else { print IFILE "<title>$var{'texttitleindex'} in Directory $dirToPrint</title>\n"; }
-:2dc8163e9150
+            Chris
-:baff1c482d98
+            Chris
    if ($var{'frames'} eq 'yes') {
        print IFILE "<base target=\"$GlobalNameFrameMainRight\" />\n";
+   }
-:2dc8163e9150
+   print IFILE "</head>\n";
-:baff1c482d98
+            Chris
-:2dc8163e9150
+   print IFILE "<body $var{'codebodyindex'}>\n";
-:675de8e6becf
+   print IFILE "<div id=\"matlabdoc\">\n";
-:2dc8163e9150
+   if ($var{'textheaderindex'} eq '') {
-:675de8e6becf
+      print IFILE "<h1 $var{'codeheader'}>Index of Matlab Files in Directory $dirToPrint</h1>\n";
-:2dc8163e9150
+   } else {
       if ($LocalGlobalLocal eq 'global') { print IFILE "<h1 $var{'codeheader'}>$var{'textheaderindex'}</h1>\n"; }
-:675de8e6becf
+      else { print IFILE "<h1 $var{'codeheader'}>$var{'textheaderindex'} in Directory $dirToPrint</h1>\n"; }
-:2dc8163e9150
+            Chris
    # include links to indexes
    &ConstructLinks2Index(IFILE, $dirnamerelpathtoindex{$LocalActDir}, $LocalActDir, $LocalGlobalLocal);
    # Collect the starting letters of m files in this directory or all m-files
    for('a'..'z') { undef @{$_}; }
    foreach $name (@localnames) {
       if (! ($mfilename{$name} =~ /contents/i)) {
          $firstletter = substr($mfilename{$name}, 0, 1);
          # convert first letter always to lower case
          # needed for reference to lower and upper case m-files
          $firstletter = "\L$firstletter\E";
          push(@{$firstletter}, $name);
+      }
+   }
    if ($LocalShortLong eq 'short') {
       # begin create short index
       print IFILE "<table width=\"100%\">\n";
       for('a'..'z') {
          # print "   $_: @{$_}\n";
          $numberofletter = $#{$_}+1;
-:675de8e6becf
+	 $cols = 3;
-:2dc8163e9150
+         if ($numberofletter > 0) {
-:675de8e6becf
+            print IFILE "\n<tr><td><br/><strong><a name=\"\U$_\E$_\"></a><span class=\"an\">\U$_\E</span></strong></td></tr>\n";
             for ($count = 0; $count < $numberofletter; $count++) {
 		if (($count % $cols) == 0) {
 		    if ($count > 0) {
 			print IFILE "</tr><tr>\n";
+		    }
 		    print IFILE "<tr><td></td>";
+		}
 		$name = @{$_}[$count];
 		if ($LocalGlobalLocal eq 'global') { $dirpath = $hfilerelpath{$name}; } else { $dirpath = ""; }
 		print IFILE "<td><a href=\"$dirpath$mfilename{$name}$var{'exthtml'}\">$mfilename{$name}</a></td>";
+	    }
 	    print IFILE "</tr>\n";
             # $numberhalf = ($numberofletter + 1 - (($numberofletter+1) % 2))/2;
             # if ($debug > 2) { print "   $_: @{$_} \t $numberhalf \t $numberofletter\n"; }
             # for($count = 0; $count < $numberhalf; $count++) {
             #    $name = @{$_}[$count];
             #    if ($LocalGlobalLocal eq 'global') { $dirpath = $hfilerelpath{$name}; } else { $dirpath = ""; }
             #    print IFILE "<tr><td width=\"50%\"><a href=\"$dirpath$mfilename{$name}$var{'exthtml'}\">$mfilename{$name}</a></td>";
             #    if (($count + $numberhalf) < $numberofletter) {
             #       $name = @{$_}[$count + $numberhalf];
             #       if ($LocalGlobalLocal eq 'global') { $dirpath = $hfilerelpath{$name}; } else { $dirpath = ""; }
             #       print IFILE "<td width=\"50%\"><a href=\"$dirpath$mfilename{$name}$var{'exthtml'}\">$mfilename{$name}</a></td></tr>\n";
             #    } else {
             #       print IFILE "<td width=\"50%\"></td></tr>\n";
             #    }
             # }
-:2dc8163e9150
+            Chris
+      }
       print IFILE "</table>\n<br />$var{'codehr'}\n";
    } elsif ($LocalShortLong eq 'long') {
       # begin create long index
-:675de8e6becf
+      print IFILE "<table width=\"100%\">\n";
-:a0f6e994657f
+      print IFILE "<tr><th>Name</th><th>Synopsis</th></tr>\n";
-:2dc8163e9150
+            Chris
       for('a'..'z') {
          # print "   $_: @{$_}\n";
          $numberofletter = $#{$_}+1;
          if ($numberofletter > 0) {
             $firstone = 1;
             foreach $name (@{$_}) {
                if ($debug > 1) { print "   AZinforeach1: $name \t\t $hfilerelpath{$name} \t\t $dirnamerelpath{$LocalActDir}\n"; }
                if ($LocalGlobalLocal eq 'global') { $dirpath = $hfilerelpath{$name}; } else { $dirpath = ""; }
                if (! ($mfilename{$name} =~ /contents/i)) {
-:4ad6499d7998
+                  if ($firstone == 1) { print IFILE "\n<tr><td colspan=\"2\"><br /><strong><a name=\"\U$_\E$_\"></a><span class=\"an\">\U$_\E</span></strong></td></tr>\n"; $firstone = 0; }
-:2dc8163e9150
+                  print IFILE "<tr><td valign=\"top\"><a href=\"$dirpath$mfilename{$name}$var{'exthtml'}\">$mfilename{$name}</a></td><td>$apropos{$name}</td></tr>\n";
+               }
+            }
+         }
+      }
       print IFILE "</table>\n<br />$var{'codehr'}\n";
    } else { die "wrong parameter for LocalShortLong in ConstructAZIndexFile: $LocalShortLong."; }
    # Include info about author from authorfile
    &WriteFile2Handle($var{'authorfile'}, IFILE);
    print IFILE "<!--navigate-->\n";
    print IFILE "<!--copyright-->\n";
-:675de8e6becf
+   print IFILE "</div>\n</body>\n</html>\n";
-:2dc8163e9150
+            Chris
    close(IFILE);
    if ($opt_silent) { print "\r"; }
    print "   Indexfile small (A-Z) created: $indexfile\t";
    if (!$opt_silent) { print "\n"; }
    # Build the A-Z jump index file name
    # handle the global index file case separately (no extra directory name in file)
    if ($LocalGlobalLocal eq 'global') { $extradirfilename = ''; }
    else { $extradirfilename = $dirnamesingle{$LocalActDir}; }
-:baff1c482d98
+   if ($var{'frames'} eq 'yes') {
        $indexfile = $var{'dirhtml'}.$dirnamerelpath{$LocalActDir}.$indexfilename.$var{'filenameextensionjump'}.$extradirfilename.$var{'exthtml'};
        if ($debug > 2) { print "   indexfilename (a-z jump): $indexfile\n"; }
        open(IFILE,">$indexfile") || die("Cannot open jump index file $indexfile: $!\n");
        # Write the header of HTML file
        print IFILE "$TextDocTypeHTML\n<html>\n<head>\n$var{'codeheadmeta'}\n$TextMetaCharset\n$var{'csslink'}\n";
        if ($var{'texttitleindex'} eq '') {
-:675de8e6becf
+	   print IFILE "<title>A-Z jump index in directory $dirToPrint</title>\n";
-:baff1c482d98
+       } else {
 	   if ($LocalGlobalLocal eq 'global') { print IFILE "<title>$var{'texttitleindex'}</title>\n"; }
-:675de8e6becf
+	   else { print IFILE "<title>$var{'texttitleindex'} in Directory $dirToPrint</title>\n"; }
-:baff1c482d98
+            Chris
        if ($var{'frames'} eq 'yes') {
 	   print IFILE "<base target=\"$GlobalNameFrameAZIndexsmall\" />\n";
+       }
        print IFILE "</head>\n";
        print IFILE "<body $var{'codebodyindex'}>\n";
-:675de8e6becf
+       print IFILE "<div id=\"matlabdoc\">\n";
-:baff1c482d98
+            Chris
        # Write the A-Z jump line, generate link for letters with files starting with this letter
        # and only letters for no files starting with this letter
        # use previously generated arrays with names of files sorted by starting letter
        for('a'..'z') {
 	   $numberofletter = $#{$_}+1;
 	   if ($numberofletter > 0) {
 	       print IFILE "<strong><a href=\"$indexfilename$var{'filenameextensionindex'}$extradirfilename$var{'exthtml'}#\U$_\E$_\">\U$_\E</a> </strong>\n";
 	   } else {
 	       print IFILE "\U$_\E \n";
+	   }
+       }
-:675de8e6becf
+       print IFILE "</div></body>\n</html>\n";
-:baff1c482d98
+            Chris
        close(IFILE);
        if ($opt_silent) { print "\r"; }
        print "   Indexfile small (A-Z jump) created: $indexfile\t";
        if (!$opt_silent) { print "\n"; }
-:2dc8163e9150
+            Chris
    # Build the frame layout file, this file includes the layout of the frames
    # Build the frame layout file name (for small/compact A-Z index)
    # handle the global index file case separately (no extra directory name in file)
    if ($LocalGlobalLocal eq 'global') { $extradirfilename = ''; }
    else { $extradirfilename = $dirnamesingle{$LocalActDir}; }
-:baff1c482d98
+   if ($var{'frames'} eq 'yes') {
-:2dc8163e9150
+            Chris
-:baff1c482d98
+       $indexfile = $var{'dirhtml'}.$dirnamerelpath{$LocalActDir}.$indexfilename.$var{'filenameextensionframe'}.$extradirfilename.$var{'exthtml'};
        if ($debug > 2) { print "   indexfilename (a-z frame): $indexfile\n"; }
-:2dc8163e9150
+            Chris
-:baff1c482d98
+       open(IFILE,">$indexfile") || die("Cannot open jump index frame file $indexfile: $!\n");
        # Write the header of Frame file
        print IFILE "$TextDocTypeHTML\n<html>\n<head>\n$var{'codeheadmeta'}\n$TextMetaCharset\n$var{'csslink'}\n";
        if ($var{'texttitleindex'} eq '') {
-:675de8e6becf
+	   print IFILE "<title>Index of Matlab Files in Directory $dirToPrint</title>\n";
-:baff1c482d98
+       } else {
 	   if ($LocalGlobalLocal eq 'global') { print IFILE "<title>$var{'texttitleindex'}</title>\n"; }
-:675de8e6becf
+	   else { print IFILE "<title>$var{'texttitleindex'} in Directory $dirToPrint</title>\n"; }
-:baff1c482d98
+            Chris
        print IFILE "</head>\n";
        # definition of 2 frames, top the A-Z index, below the jump letter line
        print IFILE "<frameset  rows=\"90%,10%\">\n";
        print IFILE "   <frame src=\"$indexfilename$var{'filenameextensionindex'}$extradirfilename$var{'exthtml'}\" name=\"$GlobalNameFrameAZIndexsmall\" />\n";
        print IFILE "   <frame src=\"$indexfilename$var{'filenameextensionjump'}$extradirfilename$var{'exthtml'}\" name=\"$GlobalNameFrameAZIndexjump\" />\n";
        print IFILE "</frameset>\n";
        print IFILE "</html>\n";
        close(IFILE);
        if ($opt_silent) { print "\r"; }
        print "   Frame layout file created: $indexfile\t";
        if (!$opt_silent) { print "\n"; }
-:2dc8163e9150
+            Chris
+}
-:baff1c482d98
+            Chris
-:2dc8163e9150
+            Chris
 #========================================================================
 # Construct the links to all indexes
 #========================================================================
 sub ConstructLinks2Index
+{
    local(*WRITEFILE, $LocalPath2Index, $PathContents, $LocalGlobalLocal) = @_;
    # include links to short/long - local/global index and C|contents.m
-:0bc92382a86b
+   print WRITEFILE "\n<p>";
    print WRITEFILE "$var{'textjumpindexglobal'} ";
-:baff1c482d98
+            Chris
    if ($var{'frames'} eq 'yes') {
        print WRITEFILE "<a href=\"$LocalPath2Index$var{'filenameindexshortglobal'}$var{'filenameextensionframe'}$var{'exthtml'}\">short</a> | ";
-:0bc92382a86b
+       print WRITEFILE "<a href=\"$LocalPath2Index$var{'filenameindexlongglobal'}$var{'filenameextensionframe'}$var{'exthtml'}\">long</a>\n";
-:baff1c482d98
+   } else {
-:f89765996ef9
+       print WRITEFILE "<a href=\"$LocalPath2Index$var{'filenametopframe'}$var{'exthtml'}\">short</a> | ";
-:0bc92382a86b
+       print WRITEFILE "<a href=\"$LocalPath2Index$var{'filenameindexlongglobal'}$var{'filenameextensionindex'}$var{'exthtml'}\">long</a>\n";
-:baff1c482d98
+            Chris
-:2dc8163e9150
+   if ($LocalGlobalLocal eq 'local') {
       if ($var{'usecontentsm'} eq 'yes') {
          print WRITEFILE " | <a href=\"$contentsname{$PathContents}$dirnamesingle{$PathContents}$var{'exthtml'}\">Local contents</a>\n";
+      }
-:0bc92382a86b
+      if ($var{'frames'} eq 'yes') {
          print WRITEFILE " | $var{'textjumpindexlocal'} ";
-:baff1c482d98
+         print WRITEFILE "<a href=\"$var{'filenameindexshortlocal'}$var{'filenameextensionframe'}$dirnamesingle{$PathContents}$var{'exthtml'}\">short</a> | ";
-:0bc92382a86b
+         print WRITEFILE "<a href=\"$var{'filenameindexlonglocal'}$var{'filenameextensionframe'}$dirnamesingle{$PathContents}$var{'exthtml'}\">long</a>\n";
       } else {
          print WRITEFILE " | $var{'textjumpindexlocal'} ";
          print WRITEFILE "<a href=\"$var{'filenameindexshortlocal'}$var{'filenameextensionindex'}$dirnamesingle{$PathContents}$var{'exthtml'}\">short</a> | ";
          print WRITEFILE "<a href=\"$var{'filenameindexlonglocal'}$var{'filenameextensionindex'}$dirnamesingle{$PathContents}$var{'exthtml'}\">long</a>\n";
+      }
-:2dc8163e9150
+            Chris
    print WRITEFILE "</p>\n\n";
    print WRITEFILE "$var{'codehr'}\n";
+}
 #========================================================================
 # Construct the contents.m files or update
 #========================================================================
 sub ConstructContentsmFile
+{
    local($LocalActDir, @localnames) = @_;
    local(*CFILE, $name,$newline);
    local($contentsfile, $isincontentsonly);
    local(@lines, @autoaddlines, @emptylines);
    local($autoadd) = 'AutoAdd';
    local($autoaddsection) = 0;
    local($emptylineflag) = 0;
    local(%nameincontents);
    # Build the contents file name
    $contentsfile = $LocalActDir.$contentsname{$LocalActDir}.$suffix;
    if (-e $contentsfile) {
       open(CFILE,"<$contentsfile") || die("Cannot open contents file $contentsfile: $!\n");
       while (<CFILE>) {
          # Search for the specified string pattern
          @words = split;
          if ((@words >= 3) && ($words[2] eq '-')) {
             $isincontentsonly = 0;
             foreach $name (@localnames) {
                if ($name eq $words[1]) {    # old
                # if ($mfilename{$name} eq $words[1]) {
                   $isincontentsonly = 1;
                   $nameincontents{$name} = 1;
                   $newline = sprintf("%% %-13s - %s\n", $mfilename{$name}, $apropos{$name});
                   push(@lines, $newline);
+               }
+            }
             # issue a warning, if file is in contents, but not as file in the directory
             if ($isincontentsonly == 0) {
                print "\rConstructContents: Obsolete entry  $words[1]  in  $contentsfile ! Entry not used.\n";
+            }
          } else {
             # look for the AutoAdd section, should be the second word
             if ((@words >= 2) && ($words[1] eq $autoadd)) { $autoaddsection = 1; }
             # push the red line in an array
             push(@lines, $_);
+         }
+      }
       close(CFILE);
    } else {
       $newline = "% MATLAB Files in directory  $LocalActDir\n%\n";
       push(@lines, $newline);
+   }
    # collect the file names, that were not included in original C|contents.m
    foreach $name (@localnames) {
       if (! defined $nameincontents{$name}) {
          if (! ($mfilename{$name} =~ /contents/i)) {
             $newline = sprintf("%% %-13s - %s\n", $mfilename{$name}, $apropos{$name});
             push(@autoaddlines, $newline);
+         }
+      }
+   }
    # write/update C|contents.m only if variable is set
    if ($var{'writecontentsm'} eq 'yes') {
       unlink($contentsfile);
       open(CFILE,">$contentsfile") || die("Cannot open contents file $contentsfile: $!\n");
       # write old C|contents.m or header of new file, as long as comment lines
       foreach $line (@lines) {
          if ($emptylineflag == 0) {
             if ($line =~ /^\s*%/) { print CFILE $line; }
             else { $emptylineflag = 1; push(@emptylines, $line); }
          } else { push(@emptylines, $line); }
+      }
       # add header of AutoAdd section
       if (($autoaddsection == 0) && (@autoaddlines > 0)) { print CFILE "%\n% $autoadd\n"; }
       # add autoadd section lines (previously undocumented files
       foreach $line (@autoaddlines) { print CFILE $line; }
       # add tail of original C|contents.m (everything behind first non-comment line)
       foreach $line (@emptylines)   { print CFILE $line; }
       print CFILE "\n";
       close CFILE;
       if ($opt_silent) { print "\r"; }
       print "   Contents file created/updated: $contentsfile\t";
       if (!$opt_silent) { print "\n"; }
+   }
+}
 #========================================================================
 # Replace found special characters with their HTMl Entities
 #========================================================================
 sub SubstituteHTMLEntities {
    local($_) = @_;
    # Replace & <-> &amp;  < <-> &lt;  > <-> &gt;  " <-> &quot;
    s/&/&amp;/g; s/\</&lt;/g; s/\>/&gt;/g; s/\"/&quot;/g;
    return $_;
+}
 #========================================================================
 # Replace found m-filenamestring with full link.
 #========================================================================
 sub SubstituteName2Link {
    local($_, $funname) = @_;
    local($refstr1, $refstr2, $reffound);
    # Look for something matching in the line
    if ( /(\W+)($funname)(\W+)/i ) {
       $reffound = $2;
-:dad587ecb8d0
+      $refstr1 = "<a class=\"mfun\" href=\"$hfileindexpath{$name}$hfilerelpath{$funname}$mfilename{$funname}$var{'exthtml'}\">";
-:2dc8163e9150
+      $refstr2 = "<\/a>";
       # Do links only for exact case match
       if ( ($var{'links2filescase'}  eq 'exact') || ($var{'links2filescase'}  eq 'exactvery') ) {
          if ( /(\W+)($funname)(\W+)/g ) {
             s/(\W+)($funname)(\W+)/$1$refstr1$funname$refstr2$3/g;
+         }
          else {
             # Print info for not matching case in references, good for check up of files
             if ( ($var{'links2filescase'}  eq 'exactvery') ) {
                print "Diff in case found: $funname  (case of file name)   <->  $reffound  (case in source code)\n";
                print "     (source line)  $_ \n";
+            }
+         }
+      }
       # Do links for exact match and additionally for all upper case (often used in original matlab help text)
       elsif ( ($var{'links2filescase'}  eq 'exactupper') ) {
          s/(\W+)($funname)(\W+)/$1$refstr1$2$refstr2$3/g;
          $funname2 = "\U$funname\E";
          s/(\W+)($funname2)(\W+)/$1$refstr1$2$refstr2$3/g;
+      }
       # Do links for all case mixes, this calls for trouble under LINUX/UNIX
       else {  #elsif ( ($var{'links2filescase'}  eq 'all') )
          s/(\W+)($funname)(\W+)/$1$refstr1$2$refstr2$3/ig;
+      }
+   }
    return $_;
+}
 #========================================================================
 # Construct the html files for each matlab file.
 #    Need to reread each matlab file to find the help text.
 #    Note that we can't do this in a single loop because sometimes
 #    the help text maybe before the function declaration.
 #========================================================================
 sub ConstructHTMLFiles
+{
    local(*MFILE);
    local(*HFILE);
    local($filescreated) = 0;
    local($functionline);
    foreach $name (@names) {
       # Create cross reference information already here, used for keywords as well
       # Construct list of referenced functions
       @xref = @{'depcalls'.$name};    # the functions, that this m-file calls
       @yref = @{'depcalled'.$name};   # the functions, that this m-file is called from
       # print "   depcalls: @{'depcalls'.$name}\n   depcalled: @{'depcalled'.$name}\n";
       # foreach $cname (@names) { next if $cname eq $name; push(@yref,$cname) if grep(/$name/,@{'depcalls'.$cname}); }
       # Open m-file and html-file
       open(MFILE,"<$mfile{$name}");
       open(HFILE,">$hfile{$name}");
       # Write the header of HTML file
       print HFILE "$TextDocTypeHTML\n<html>\n<head>\n$var{'codeheadmeta'}\n$TextMetaCharset\n$var{'csslink'}\n";
       # Write meta tags: use apropos (one line function description) for description
       # and cross reference function names for keywords (any better ideas?)
       print HFILE "<meta name=\"description\" content=\" $apropos{$name} \" />\n";
       print HFILE "<meta name=\"keywords\" content=\" @xref @yref \" />\n";
       # Write Title and start body of html-file
       print HFILE "<title>$var{'texttitlefiles'} $mfilename{$name}</title>\n</head>\n";
       print HFILE "<body $var{'codebodyfiles'}>\n";
-:675de8e6becf
+      print HFILE "<div id=\"matlabdoc\">\n";
-:2dc8163e9150
+      print HFILE "<h1 $var{'codeheader'}>$var{'textheaderfiles'} $mfilename{$name}</h1>\n";
-:a0f6e994657f
+            chris
 # http://test.soundsoftware.ac.uk/cannam/projects/smallbox/repository/annotate/DL/RLS-DLA/SolveFISTA.m
-:675de8e6becf
+#      print HFILE "<a href=\"" . $hfileindexpath{$name} . "../../projects/smallbox/repository/annotate/" . $mfiledir{$name}  . $mfilename{$name} . ".m\">View in repository</a>\n";
-:a0f6e994657f
+            chris
-:2dc8163e9150
+      print HFILE "$var{'codehr'}\n";
       # include links to short/long - local/global index and C|contents.m
       &ConstructLinks2Index(HFILE, $hfileindexpath{$name}, $mfiledir{$name}, 'local');
       # If this is a function, then write out the first line as a synopsis
       if ($mtype{$name} eq "function") {
          print HFILE "<h2 $var{'codeheader'}>Function Synopsis</h2>\n";
          print HFILE "<pre>$synopsis{$name}</pre>\n$var{'codehr'}\n";
+      }
       # Look for the matlab help text block
       $functionline = "\n";
       do {
          $_ = <MFILE>;
          # remember functionline, if before help text block
          if (/^\s*function/) { $functionline = $_; }
       } until (/^\s*%/ || eof);
       if (! (eof(MFILE))) {
          print HFILE "<h2 $var{'codeheader'}>Help text</h2>\n";
          print HFILE "<pre>\n";
          while (/^\s*%/) {
             # First remove leading % and white space, then Substitute special characlers
             s/^\s*%//;
             $_ = &SubstituteHTMLEntities($_);
             # check/create cross references
             foreach $funname (@{'all'.$name}) {
                if ($funname =~ /simulink/) { print "\n Simulink - Filename: $name;  scanname: $funname\n"; }
                next if $funname eq $name;
                $_ = &SubstituteName2Link($_, $funname);
+            }
             print HFILE $_;
             if (! eof) { $_ = <MFILE>; }
+         }
          print HFILE "</pre>\n$var{'codehr'}\n";
+      }
       # Write the cross reference information
       if (@xref || @yref) {
          print HFILE "<h2 $var{'codeheader'}>Cross-Reference Information</H2>\n";
          print HFILE "<table border=\"0\" width=\"100%\">\n<tr align=\"left\">\n<th width=\"50%\">";
          if (@xref) {
             print HFILE "This $mtype{$name} calls";
+         }
          print HFILE "</th>\n<th width=\"50%\">";
          if (@yref) {
             print HFILE "This $mtype{$name} is called by";
+         }
          print HFILE "</th>\n</tr>\n<tr valign=\"top\"><td>";
          if (@xref) {
             print HFILE "\n<ul>\n";
             foreach $cname (sort @xref) {
                print HFILE "<li><a class=\"mfun\" href=\"$hfileindexpath{$name}$hfilerelpath{$cname}$mfilename{$cname}$var{'exthtml'}\">$mfilename{$cname}</a></li>\n";
+            }
             print HFILE "</ul>\n";
+         }
          print HFILE "</td><td>";
          if (@yref) {
             print HFILE "\n<ul>\n";
             foreach $cname (sort @yref) {
                print HFILE "<li><a class=\"mfun\" href=\"$hfileindexpath{$name}$hfilerelpath{$cname}$mfilename{$cname}$var{'exthtml'}\">$mfilename{$cname}</a></li>\n";
+            }
             print HFILE "</ul>\n";
+         }
          print HFILE "</td>\n</tr>\n</table>\n";
          print HFILE "$var{'codehr'}\n";
+      }
       # Include source text if requested
       if (($var{'includesource'} eq 'yes') && (! ($mfilename{$name} =~ /^contents$/i))) {
          print HFILE "<h2 $var{'codeheader'}>Listing of $mtype{$name} $mfilename{$name}</h2>\n";
          seek(MFILE,0,0);
          print HFILE "<pre>\n";
          $IsStillHelp = 2;
          print HFILE $functionline;    # functionline from scanning of help
          while (<MFILE>) {
             if ($IsStillHelp == 2) {
                next     if (/^\s*$/);
                next     if (/^\s*function/);
                if (/^\s*%/) { $IsStillHelp = 1; next; }
             } elsif ($IsStillHelp == 1) {
                next     if (/^\s*%/);
                $IsStillHelp = 0;
+            }
             # Substritute special characters
             $_ = &SubstituteHTMLEntities($_);
             # check for comment in line and format with css em
-:4ad6499d7998
+            s/^(.*)%(.*?)([\s\r\n]+)$/$1<em class=\"mcom\">%$2<\/em>$3/;
-:2dc8163e9150
+            Chris
             # check/create cross references
             foreach $funname (@{'all'.$name}) {
                next if $funname eq $name;
                $_ = &SubstituteName2Link($_, $funname);
+            }
             print HFILE $_;
+         }
          print HFILE "</pre>\n$var{'codehr'}\n";
+      }
       # Include info about author from authorfile
       &WriteFile2Handle($var{'authorfile'}, HFILE)   ;
       print HFILE "<!--navigate-->\n";
       print HFILE "<!--copyright-->\n";
-:675de8e6becf
+      print HFILE "</div>\n</body>\n</html>\n";
-:2dc8163e9150
+      close(MFILE);
       close(HFILE);
       # Print name of finished file
       if ($opt_silent) { print "\r"; }
       print "   HTML-File created: $hfile{$name}\t";
       if (!$opt_silent) { print "\n"; }
       $filescreated++;
+   }
    print "\n$PROGRAM: $indexcreated index and $filescreated files created.\n";
+}
 #========================================================================
 # Function:	CheckFileName
 # Purpose:	.
 #========================================================================
 sub CheckFileName {
    local($filename, $description) = @_;
    local(*CHECKFILE);
    open(CHECKFILE,"<$filename") || do {
       if ($description eq '') {$description = 'file';}
       # if (!$opt_silent) { print "Cannot open $description $filename: $!\n"; }
       print "Cannot open $description $filename: $!\n";
       return 1;
    };
    close(CHECKFILE);
    return 0;
+}
 #========================================================================
 # Function:	CheckDirName
 # Purpose:	.
 #========================================================================
 sub CheckDirName {
    local($dirname, $description) = @_;
    local(*CHECKDIR);
    opendir(CHECKDIR,"$dirname") || die ("Cannot open $description directory $dirname: $!\n");
    closedir(CHECKDIR);
+}
 #========================================================================
 # Function:	WriteFile2Handle
 # Purpose:	.
 #========================================================================
 sub WriteFile2Handle {
    local($filename, *WRITEFILE) = @_;
    local(*READFILE);
    if ($filename ne '') {
       open(READFILE,"<$filename");
       @filecontents = <READFILE>;
       close(READFILE);
       print WRITEFILE "@filecontents\n";
       # if (!$opt_silent) {print "      Contents of $filename added\n"};
+   }
+}
 #========================================================================
 # Function:	GetConfigFile
 # Purpose:	Read user's configuration file, if such exists.
 #========================================================================
 sub GetConfigFile
+{
    local($filename) = @_;
    local(*CONFIG);
    local($value);
    if (&CheckFileName($filename, 'configuration file')) {
       # if (!$opt_silent) { print "   Proceeding using built-in defaults for configuration.\n"; }
       print "   Proceeding using built-in defaults for configuration.\n";
       return 0;
    };
    open(CONFIG,"< $filename");
    while (<CONFIG>) {
       s/#.*$//;
       next if /^\s*$/o;
       # match keyword: process one or more arguments
       # keyword set
       if (/^\s*set\s+(\S+)\s*=\s*(.*)/) {
          # setting a configuration variable
          if (defined $var{$1}) {
             $var{$1} = $2;
             if ($debug > 3) { print "$1:   $var{$1}\n"; }
+         }
          else {
             print "$PROGRAM: unknown variable `$1' in configuration file\n"
+         }
       } else {
          chop($_);
          print "$PROGRAM: unknown keyword in configuration file in line: `$_'\n"
+      }
+   }
    close CONFIG;
 ;
+}
 #------------------------------------------------------------------------
 # DisplayHelp - display help text using -h or -help command-line switch
 #------------------------------------------------------------------------
 sub DisplayHelp
+{
    $help=<<EofHelp;
    $PROGRAM v$VERSION - generate html documentation from Matlab m-files
    Usage: $PROGRAM [-h] [-c config_file] [-m|dirmfiles matlab_dir] [-d|dirhtml html_dir]
                    [-i yes|no] [-r yes|no] [-p yes|no] [-quiet|q] [-a authorfile]
    $PROGRAM is a perl script that reads each matlab .m file in a directory
    to produce a corresponding .html file of help documentation and cross
    reference information. An index file is written with links to all of
    the html files produced. The options are:
       -quiet         or -q : be silent, no status information during generation
       -help          or -h : display this help message
       -todo          or -t : print the todo list for $PROGRAM
       -version       or -v : display version
       -configfile    or -c : name of configuration file (default to $var{'configfile'}).
       -dirmfiles     or -m : top level directory containing matlab files to generate html for;
                              default to actual directory.
       -dirhtml       or -d : top level directory for generated html files;
                              default to actual directory.
       -includesource or -i : Include matlab source in the html documentation [yes|no]
                              default to yes.
       -processtree   or -r : create docu for m-file directory and all subdirectories [yes|no];
                              default to yes.
       -producetree   or -p : create multi-level docu identical to directory structure
                              of m-files [yes|no]; default to yes.
       -writecontentsm or -w: update or write contents.m files into the matlab source
                              directories [yes|no]; default to no.
       -authorfile    or -a : name of file including author information, last element in html;
                              default to empty.
    The command line setting overwrite all other settings (built-in and configuration file).
    The configuration file settings overwrite the built-in settings (and not the command
    line settings).
    Typical usages are:
      $PROGRAM
         (use default parameters from perl script, if configuration
          file is found -> generation of docu, else display of help)
      $PROGRAM -dirmfiles matlab -dirhtml html
         (generate html documentation for all m-files in directory matlab,
          place html files in directory html, use built-in defaults for
          all other parameters, this way all m-files in the directory
          matlab and below are converted and the generated html-files are
          placed in the directory html and below producing the same
          directory structure than below matlab)
      $PROGRAM -quiet
         (use built-in parameters from perl script, if configuration
          file is found use these settings as well, do generation,
          no display except critical errors, status of conversion and result)
      $PROGRAM -m toolbox -dirhtml doc/html -r yes -p no
         (convert all m-files in directory toolbox and below and place
          the generated html files in directory doc/html, read all m-files
          recursively, however, the generated html files are placed in one
          directory)
      $PROGRAM -m toolbox -dirhtml doc/html -i no -r no
         (convert all m-files in directory toolbox and place
          the generated html files in directory doc/html, do not read m-files
          recursively, do not include source code in documentation)
 EofHelp
    die "$help";
+}
 #------------------------------------------------------------------------
 # DisplayTodo - display ToDo list using -t or -todo command-line switch
 #------------------------------------------------------------------------
 sub DisplayTodo
+{
    $todo=<<EofToDo;
       $PROGRAM v$VERSION - ToDo list
        o	use more than one high level directory
        o	what should/could be done here???
 EofToDo
    die "$todo";
+}
 #------------------------------------------------------------------------
 # ListVariables - list all defined variables and their values
 #------------------------------------------------------------------------
 sub ListVariables
+{
    local($value);
    if ($debug > 0) {
       print "List of all variables and their values\n";
       foreach (sort keys %var)
+      {
          if ($var{$_} eq '') {
             $value = "empty";
          } else {
             $value = $var{$_};
+         }
          print "   $_\n      $value\n";
+      }
       print "\n\n";
+   }
+}
 __END__
 :endofperl
-:513646585e45
+#!/usr/bin/env ruby
 # == Synopsis
+#
 # reposman: manages your repositories with Redmine
+#
 # == Usage
+#
 #    reposman [OPTIONS...] -s [DIR] -r [HOST]
-:cbce1fd3b1b7
+            Chris
-:513646585e45
+#  Examples:
-:7658d21a1493
+#    reposman --scm-dir=/var/svn --redmine-host=redmine.example.net --scm subversion
-:513646585e45
+#    reposman -s /var/git -r redmine.example.net -u http://svn.example.net --scm git
+#
 # == Arguments (mandatory)
+#
-:7658d21a1493
+#   -s, --scm-dir=DIR         use DIR as base directory for repositories
-:513646585e45
+#   -r, --redmine-host=HOST   assume Redmine is hosted on HOST. Examples:
 #                             -r redmine.example.net
 #                             -r http://redmine.example.net
 #                             -r https://example.net/redmine
-:cbb26bc654de
+#   -k, --key=KEY             use KEY as the Redmine API key (you can use the
 #                             --key-file option as an alternative)
-:513646585e45
+            Chris
 # == Options
+#
 #   -o, --owner=OWNER         owner of the repository. using the rails login
 #                             allow user to browse the repository within
 #                             Redmine even for private project. If you want to
 #                             share repositories through Redmine.pm, you need
 #                             to use the apache owner.
 #   -g, --group=GROUP         group of the repository. (default: root)
 #   --scm=SCM                 the kind of SCM repository you want to create (and
 #                             register) in Redmine (default: Subversion).
 #                             reposman is able to create Git and Subversion
 #                             repositories. For all other kind, you must specify
 #                             a --command option
 #   -u, --url=URL             the base url Redmine will use to access your
 #                             repositories. This option is used to automatically
 #                             register the repositories in Redmine. The project
 #                             identifier will be appended to this url. Examples:
 #                             -u https://example.net/svn
 #                             -u file:///var/svn/
-:12420e46bed9
+#                             if this option isn't set, reposman will register
 #                             the repositories with local file paths in Redmine
-:513646585e45
+#   -c, --command=COMMAND     use this command instead of "svnadmin create" to
 #                             create a repository. This option can be used to
 #                             create repositories other than subversion and git
 #                             kind.
 #                             This command override the default creation for git
 #                             and subversion.
-:80433603a2cd
+#   --http-user=USER          User for HTTP Basic authentication with Redmine WS
 #   --http-pass=PASSWORD      Password for Basic authentication with Redmine WS
-:cbb26bc654de
+#       --key-file=PATH       path to a file that contains the Redmine API key
 #                             (use this option instead of --key if you don't
 #                             the key to appear in the command line)
-:513646585e45
+#   -t, --test                only show what should be done
 #   -h, --help                show help and exit
 #   -v, --verbose             verbose
 #   -V, --version             print version and exit
 #   -q, --quiet               no log
+#
 # == References
-:cbce1fd3b1b7
+            Chris
-:513646585e45
+# You can find more information on the redmine's wiki : http://www.redmine.org/wiki/redmine/HowTos
 require 'getoptlong'
-:1d1cb01c0417
+#require 'rdoc/usage'
-:513646585e45
+require 'find'
 require 'etc'
 Version = "1.3"
 SUPPORTED_SCM = %w( Subversion Darcs Mercurial Bazaar Git Filesystem )
 opts = GetoptLong.new(
-:7658d21a1493
+                      ['--scm-dir',      '-s', GetoptLong::REQUIRED_ARGUMENT],
-:513646585e45
+                      ['--redmine-host', '-r', GetoptLong::REQUIRED_ARGUMENT],
                       ['--key',          '-k', GetoptLong::REQUIRED_ARGUMENT],
-:cbb26bc654de
+                      ['--key-file',           GetoptLong::REQUIRED_ARGUMENT],
-:513646585e45
+                      ['--owner',        '-o', GetoptLong::REQUIRED_ARGUMENT],
                       ['--group',        '-g', GetoptLong::REQUIRED_ARGUMENT],
                       ['--url',          '-u', GetoptLong::REQUIRED_ARGUMENT],
                       ['--command' ,     '-c', GetoptLong::REQUIRED_ARGUMENT],
                       ['--scm',                GetoptLong::REQUIRED_ARGUMENT],
-:80433603a2cd
+                      ['--http-user',          GetoptLong::REQUIRED_ARGUMENT],
                       ['--http-pass',          GetoptLong::REQUIRED_ARGUMENT],
-:513646585e45
+                      ['--test',         '-t', GetoptLong::NO_ARGUMENT],
                       ['--verbose',      '-v', GetoptLong::NO_ARGUMENT],
                       ['--version',      '-V', GetoptLong::NO_ARGUMENT],
                       ['--help'   ,      '-h', GetoptLong::NO_ARGUMENT],
                       ['--quiet'  ,      '-q', GetoptLong::NO_ARGUMENT]
+                      )
 $verbose      = 0
 $quiet        = false
 $redmine_host = ''
 $repos_base   = ''
-:80433603a2cd
+$http_user    = ''
 $http_pass    = ''
-:513646585e45
+$svn_owner    = 'root'
 $svn_group    = 'root'
 $use_groupid  = true
 $svn_url      = false
 $test         = false
 $scm          = 'Subversion'
 def log(text, options={})
   level = options[:level] || 0
   puts text unless $quiet or level > $verbose
   exit 1 if options[:exit]
 end
 def system_or_raise(command)
   raise "\"#{command}\" failed" unless system command
 end
-:1d1cb01c0417
+def usage
   puts "See source code for supported options"
   exit
 end
-:513646585e45
+module SCM
   module Subversion
     def self.create(path)
       system_or_raise "svnadmin create #{path}"
     end
   end
   module Git
     def self.create(path)
       Dir.mkdir path
       Dir.chdir(path) do
         system_or_raise "git --bare init --shared"
         system_or_raise "git update-server-info"
       end
     end
   end
 end
 begin
   opts.each do |opt, arg|
     case opt
-:7658d21a1493
+    when '--scm-dir';        $repos_base   = arg.dup
-:513646585e45
+    when '--redmine-host';   $redmine_host = arg.dup
     when '--key';            $api_key      = arg.dup
-:cbb26bc654de
+    when '--key-file'
       begin
         $api_key = File.read(arg).strip
       rescue Exception => e
         $stderr.puts "Unable to read the key from #{arg}: #{e.message}"
         exit 1
       end
-:513646585e45
+    when '--owner';          $svn_owner    = arg.dup; $use_groupid = false;
     when '--group';          $svn_group    = arg.dup; $use_groupid = false;
     when '--url';            $svn_url      = arg.dup
     when '--scm';            $scm          = arg.dup.capitalize; log("Invalid SCM: #{$scm}", :exit => true) unless SUPPORTED_SCM.include?($scm)
-:80433603a2cd
+    when '--http-user';      $http_user    = arg.dup
     when '--http-pass';      $http_pass    = arg.dup
-:513646585e45
+    when '--command';        $command =      arg.dup
     when '--verbose';        $verbose += 1
     when '--test';           $test = true
     when '--version';        puts Version; exit
-:1d1cb01c0417
+    when '--help';           usage
-:513646585e45
+    when '--quiet';          $quiet = true
     end
   end
 rescue
   exit 1
 end
 if $test
   log("running in test mode")
 end
 # Make sure command is overridden if SCM vendor is not handled internally (for the moment Subversion and Git)
 if $command.nil?
   begin
     scm_module = SCM.const_get($scm)
   rescue
     log("Please use --command option to specify how to create a #{$scm} repository.", :exit => true)
   end
 end
 $svn_url += "/" if $svn_url and not $svn_url.match(/\/$/)
 if ($redmine_host.empty? or $repos_base.empty?)
-:1d1cb01c0417
+  usage
-:513646585e45
+end
 unless File.directory?($repos_base)
-:ed8222a04634
+  log("directory '#{$repos_base}' doesn't exist", :exit => true)
-:513646585e45
+end
 begin
   require 'active_resource'
 rescue LoadError
   log("This script requires activeresource.\nRun 'gem install activeresource' to install it.", :exit => true)
 end
-:94944d00e43c
+class Project < ActiveResource::Base
-:ed8222a04634
+  self.headers["User-agent"] = "SoundSoftware repository manager/#{Version}"
-:cbb26bc654de
+  self.format = :xml
-:94944d00e43c
+end
-:513646585e45
+            Chris
 log("querying Redmine for projects...", :level => 1);
 $redmine_host.gsub!(/^/, "http://") unless $redmine_host.match("^https?://")
 $redmine_host.gsub!(/\/$/, '')
 Project.site = "#{$redmine_host}/sys";
-:80433603a2cd
+Project.user = $http_user;
 Project.password = $http_pass;
-:513646585e45
+            Chris
 begin
   # Get all active projects that have the Repository module enabled
   projects = Project.find(:all, :params => {:key => $api_key})
-:cbb26bc654de
+rescue ActiveResource::ForbiddenAccess
   log("Request was denied by your Redmine server. Make sure that 'WS for repository management' is enabled in application settings and that you provided the correct API key.")
-:513646585e45
+rescue => e
   log("Unable to connect to #{Project.site}: #{e}", :exit => true)
 end
 if projects.nil?
-:cbb26bc654de
+  log('No project found, perhaps you forgot to "Enable WS for repository management"', :exit => true)
-:513646585e45
+end
-:4f45ab104990
+log("found #{projects.size} projects at " + Time.now.inspect);
-:513646585e45
+            Chris
 def set_owner_and_rights(project, repos_path, &block)
-:cbce1fd3b1b7
+  if mswin?
-:513646585e45
+    yield if block_given?
   else
     uid, gid = Etc.getpwnam($svn_owner).uid, ($use_groupid ? Etc.getgrnam(project.identifier).gid : Etc.getgrnam($svn_group).gid)
-:09b1d4349da3
+    right = project.is_public ? 02775 : 02770
-:513646585e45
+    yield if block_given?
     Find.find(repos_path) do |f|
       File.chmod right, f
       File.chown uid, gid, f
     end
   end
 end
 def other_read_right?(file)
   (File.stat(file).mode & 0007).zero? ? false : true
 end
 def owner_name(file)
   mswin? ?
     $svn_owner :
-:cbce1fd3b1b7
+    Etc.getpwuid( File.stat(file).uid ).name
-:513646585e45
+end
-:cbce1fd3b1b7
+            Chris
-:513646585e45
+def mswin?
   (RUBY_PLATFORM =~ /(:?mswin|mingw)/) || (RUBY_PLATFORM == 'java' && (ENV['OS'] || ENV['os']) =~ /windows/i)
 end
 projects.each do |project|
-:4f45ab104990
+  log("inspecting project #{project.name}", :level => 1)
-:513646585e45
+            Chris
   if project.identifier.empty?
-:4f45ab104990
+    log("\tno identifier for project #{project.name}!")
-:513646585e45
+    next
-:0c7b3bb73517
+  elsif not project.identifier.match(/^[a-z0-9_\-]+$/)
-:4f45ab104990
+    log("\tinvalid identifier for project #{project.name} : #{project.identifier}!");
-:513646585e45
+    next;
   end
   repos_path = File.join($repos_base, project.identifier).gsub(File::SEPARATOR, File::ALT_SEPARATOR || File::SEPARATOR)
-:12420e46bed9
+  create_repos = false
   # Logic required for SoundSoftware.ac.uk repositories:
+  #
   # * If the project has a repository path declared already,
   #   - if it's a local path,
   #     - if it does not exist
   #       - if it has the right root
   #         - create it
   #   - else
   #     - leave alone (remote repository)
   # * else
   #   - create repository with same name as project
   #   - set to project
   if project.respond_to?(:repository)
     repos_url = project.repository.url;
-:4f45ab104990
+    log("\texisting url for project #{project.identifier} is #{repos_url}", :level => 2);
-:12420e46bed9
+            chris
     if repos_url.match(/^file:\//) || repos_url.match(/^\//)
       repos_url = repos_url.gsub(/^file:\/*/, "/");
-:4f45ab104990
+      log("\tthis is a local file path, at #{repos_url}", :level => 2);
-:12420e46bed9
+            chris
       if repos_url.slice(0, $repos_base.length) != $repos_base
         # leave repos_path set to our original suggestion
-:4f45ab104990
+        log("\tpreparing to replace incorrect repo location #{repos_url} for #{project.name} with #{repos_path}");
-:12420e46bed9
+        create_repos = true
       else
         if !File.directory?(repos_url)
-:4f45ab104990
+          log("\tpreparing to create repo for #{project.name} at #{repos_url}");
-:12420e46bed9
+          repos_path = repos_url
           create_repos = true
         else
-:4f45ab104990
+          log("\tit exists and is in the right place", :level => 2);
-:12420e46bed9
+        end
       end
     else
-:4f45ab104990
+      log("\tthis is a remote path, leaving alone", :level => 2);
-:12420e46bed9
+    end
   else
-:4f45ab104990
+    log("\tpreparing to set repo location and create for #{project.name} at #{repos_url}")
-:12420e46bed9
+#    if File.directory?(repos_path)
 #      log("\trepository path #{repos_path} already exists, not creating")
 #    else
       create_repos = true
 #    end
   end
   if create_repos
     registration_url = repos_path
     if $svn_url
       registration_url = "#{$svn_url}#{project.identifier}"
     end
-:513646585e45
+            Chris
     if $test
-:12420e46bed9
+      log("\tproposal: create repository #{repos_path}")
       log("\tproposal: register repository #{repos_path} in Redmine with vendor #{$scm}, url #{registration_url}")
-:513646585e45
+      next
     end
-:8c3409528d3a
+# No -- we need "other" users to be able to read it.  Access control
 # is not handled through Unix user id anyway
 #    project.is_public ? File.umask(0002) : File.umask(0007)
     File.umask(0002)
-:12420e46bed9
+    log("\taction: create repository #{repos_path}")
-:513646585e45
+            Chris
     begin
-:12420e46bed9
+      if !File.directory?(repos_path)
         set_owner_and_rights(project, repos_path) do
           if scm_module.nil?
             log("\trunning command: #{$command} #{repos_path}")
             system_or_raise "#{$command} #{repos_path}"
           else
             scm_module.create(repos_path)
           end
-:513646585e45
+        end
       end
     rescue => e
       log("\tunable to create #{repos_path} : #{e}\n")
       next
     end
-:12420e46bed9
+    begin
       log("\taction: register repository #{repos_path} in Redmine with vendor #{$scm}, url #{registration_url}");
       project.post(:repository, :vendor => $scm, :repository => {:url => "#{registration_url}"}, :key => $api_key)
     rescue => e
       log("\trepository #{repos_path} not registered in Redmine: #{e.message}");
-:513646585e45
+    end
     log("\trepository #{repos_path} created");
   end
-:94944d00e43c
+end
-:513646585e45
+            Chris
-:4f45ab104990
+log("project review completed at " + Time.now.inspect);
-:7658d21a1493
+#!/bin/sh
-:bde4f47b6427
+mirrordir="/var/mirror"
-:b61a51fb42b9
+hg="/usr/bin/hg"
-:bde4f47b6427
+            chris
-:7658d21a1493
+project="$1"
 local_repo="$2"
 remote_repo="$3"
 if [ -z "$project" ] || [ -z "$local_repo" ] || [ -z "$remote_repo" ]; then
     echo "Usage: $0 <project> <local-repo-path> <remote-repo-url>"
     exit 2
 fi
   # We need to handle different source repository types separately.
+  #
   # The convert extension cannot convert directly from a remote git
   # repo; we'd have to mirror to a local repo first.  Incremental
   # conversions do work though.  The hg-git plugin will convert
   # directly from remote repositories, but not via all schemes
   # (e.g. https is not currently supported).  It's probably easier to
   # use git itself to clone locally and then convert or hg-git from
   # there.
+  #
   # We can of course convert directly from remote Subversion repos,
   # but we need to keep track of that -- you can ask to convert into a
   # repo that has already been used (for Mercurial) and it'll do so
   # happily; we don't want that.
+  #
   # Converting from a remote Hg repo should be fine!
+  #
   # One other thing -- we can't actually tell the difference between
   # the various SCM types based on URL alone.  We have to try them
   # (ideally in an order determined by a guess based on the URL) and
   # see what happens.
-:bde4f47b6427
+project_mirror="$mirrordir/$project"
 mkdir -p "$project_mirror"
 project_repo_mirror="$project_mirror/repo"
-:7658d21a1493
+            chris
-:bde4f47b6427
+  # Some test URLs:
+  #
   # http://aimc.googlecode.com/svn/trunk/
   # http://aimc.googlecode.com/svn/
   # http://vagar.org/git/flam
   # https://github.com/wslihgt/IMMF0salience.git
   # http://hg.breakfastquay.com/dssi-vst/
   # git://github.com/schacon/hg-git.git
   # http://svn.drobilla.net/lad (externals!)
 # If we are importing from another distributed system, then our aim is
 # to create either a Hg repo or a git repo at $project_mirror, which
 # we can then pull from directly to the Hg repo at $local_repo (using
 # hg-git, in the case of a git repo).
 # Importing from SVN, we should use hg convert directly to the target
 # hg repo (or should we?) but keep a record of the last changeset ID
 # we brought in, and test each time whether it matches the last
 # changeset ID actually in the repo
 success=""
-:4eb486dbf730
+# If we have a record of the last successfully updated remote repo
 # URL, check it against our current remote URL: if it has changed, we
 # will need to start again with a new clone rather than pulling
 # updates into the existing local mirror
 successfile="$project_mirror/last_successful_url"
 if [ -f "$successfile" ]; then
     last=$(cat "$successfile")
-:102056ec2de9
+    if [ x"$last" = x"$remote_repo" ]; then
-:4eb486dbf730
+	echo "$$: Remote URL is unchanged from last successful update"
     else
 	echo "$$: Remote URL has changed since last successful update:"
 	echo "$$: Last URL was $last, current is $remote_repo"
 	suffix="$$.$(date +%s)"
 	echo "$$: Moving existing repos to $suffix suffix and starting afresh"
 	mv "$project_repo_mirror" "$project_repo_mirror"."$suffix"
 	mv "$local_repo" "$local_repo"."$suffix"
 	mv "$successfile" "$successfile"."$suffix"
-:102056ec2de9
+	touch "$project_mirror/url_changed"
-:4eb486dbf730
+    fi
 fi
-:bde4f47b6427
+if [ -d "$project_repo_mirror" ]; then
     # Repo mirror exists: update it
     echo "$$: Mirror for project $project exists at $project_repo_mirror, updating" 1>&2
     if [ -d "$project_repo_mirror/.hg" ]; then
-:7fd72f22a42b
+	"$hg" --config extensions.convert= convert --datesort "$remote_repo" "$project_repo_mirror" && success=true
-:d3faf348b287
+	if [ -z "$success" ]; then
 	    ( cd "$project_repo_mirror" && "$hg" pull "$remote_repo" ) && success=true
 	fi
-:bde4f47b6427
+    elif [ -d "$project_repo_mirror/.git" ]; then
-:d3af621ba9d4
+	( cd "$project_repo_mirror" && git pull "$remote_repo" master ) && success=true
-:bde4f47b6427
+    else
 	echo "$$: ERROR: Repo mirror dir $project_repo_mirror exists but is not an Hg or git repo" 1>&2
     fi
 else
     # Repo mirror does not exist yet
     echo "$$: Mirror for project $project does not yet exist at $project_repo_mirror, trying to convert or clone" 1>&2
     case "$remote_repo" in
 	*git*)
 	    git clone "$remote_repo" "$project_repo_mirror" ||
-:7fd72f22a42b
+	    "$hg" --config extensions.convert= convert --datesort "$remote_repo" "$project_repo_mirror"
-:bde4f47b6427
+	    ;;
 	*)
-:7fd72f22a42b
+	    "$hg" --config extensions.convert= convert --datesort "$remote_repo" "$project_repo_mirror" ||
-:defe55be97b9
+	    git clone "$remote_repo" "$project_repo_mirror" ||
-:7fd72f22a42b
+	    "$hg" clone "$remote_repo" "$project_repo_mirror"
-:bde4f47b6427
+	    ;;
     esac && success=true
 fi
 echo "Success=$success"
 if [ -n "$success" ]; then
     echo "$$: Update successful, pulling into local repo at $local_repo"
-:4eb486dbf730
+    if [ ! -d "$local_repo" ]; then
 	"$hg" init "$local_repo"
     fi
-:bde4f47b6427
+    if [ -d "$project_repo_mirror/.git" ]; then
-:4eb486dbf730
+	( cd "$local_repo" && "$hg" --config extensions.hggit= pull "$project_repo_mirror" ) && echo "$remote_repo" > "$successfile"
-:bde4f47b6427
+    else
-:4eb486dbf730
+	( cd "$local_repo" && "$hg" pull "$project_repo_mirror" ) && echo "$remote_repo" > "$successfile"
-:bde4f47b6427
+    fi
 fi

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