--- doc/loncapafiles/loncapafiles.lpml	2002/05/05 18:08:33	1.126
+++ doc/loncapafiles/loncapafiles.lpml	2003/01/30 15:10:47	1.210
@@ -3,7 +3,7 @@
 <!-- loncapafiles.lpml -->
 <!-- Scott Harrison -->
 
-<!-- $Id: loncapafiles.lpml,v 1.126 2002/05/05 18:08:33 harris41 Exp $ -->
+<!-- $Id: loncapafiles.lpml,v 1.210 2003/01/30 15:10:47 www Exp $ -->
 
 <!--
 
@@ -140,6 +140,14 @@ http://www.lon-capa.org/
   <chmod dist='default'>0644</chmod><chown dist='default'>root:root</chown>
   <abbreviation>systemfile</abbreviation>
 </category>
+<category name="system script" type="runtime">
+  <chmod dist='default'>0755</chmod><chown dist='default'>root:root</chown>
+  <abbreviation>systemscript</abbreviation>
+</category>
+<category name="system script" type="development">
+  <chmod dist='default'>0755</chmod><chown dist='default'>root:root</chown>
+  <abbreviation>systemscript</abbreviation>
+</category>
 <category name="root script" type="runtime">
   <chmod dist='default'>0700</chmod><chown dist='default'>root:root</chown>
   <abbreviation>rootscript</abbreviation>
@@ -216,118 +224,119 @@ echo '**********************************
 <rpmRequires>
 <item>PreReq: LON-CAPA-setup</item>
 <item>PreReq: apache</item>
-<item>PreReq: /etc/httpd/conf/access.conf</item>
+<item>PreReq: /etc/httpd/conf/httpd.conf</item>
 </rpmRequires>
 </rpm>
 <directories>
 <directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>etc</targetdir>
   <categoryname>standard</categoryname>
   <description>standard linux directory for configuration files</description>
 </directory>
 <directory dist='default'>
-  <targetdir dist='default'>etc/atalk</targetdir>
-  <categoryname>standard</categoryname>
-  <description>appletalk configuration files</description>
-</directory>
-<directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>etc/cron.d</targetdir>
   <categoryname>standard</categoryname>
   <description>standard linux directory for running time-based "jobs"
   </description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>etc/httpd/conf</targetdir>
   <categoryname>standard</categoryname>
   <description>web configuration files</description>
 </directory>
 <directory dist='default'>
-  <targetdir dist='default'>etc/ntp</targetdir>
-  <categoryname>standard</categoryname>
-  <description>configuration directory for network time protocol</description>
-</directory>
-<directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>etc/pam.d</targetdir>
   <categoryname>standard</categoryname>
   <description>configuration directory for password authentication mechanism
   </description>
 </directory>
 <directory dist='default'>
-  <targetdir dist='redhat7 redhat7.1'>etc/samba</targetdir>
-  <categoryname>standard</categoryname>
-  <description>configuration directory for samba authentication
-  </description>
-</directory>
-<directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>etc/rc.d/init.d</targetdir>
-  <targetdir dist='debian2.2'>etc/init.d</targetdir>
+  <targetdir dist='debian'>etc/init.d</targetdir>
   <categoryname>standard</categoryname>
   <description>scripts that run during system startup</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>etc/rc.d/rc0.d</targetdir>
-  <targetdir dist='debian2.2'>etc/rc0.d</targetdir>
+  <targetdir dist='debian'>etc/rc0.d</targetdir>
   <categoryname>standard</categoryname>
   <description>scripts that run for run-level 0</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>etc/rc.d/rc1.d</targetdir>
-  <targetdir dist='debian2.2'>etc/rc1.d</targetdir>
+  <targetdir dist='debian'>etc/rc1.d</targetdir>
   <categoryname>standard</categoryname>
   <description>scripts that run for run-level 1</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>etc/rc.d/rc2.d</targetdir>
-  <targetdir dist='debian2.2'>etc/rc2.d</targetdir>
+  <targetdir dist='debian'>etc/rc2.d</targetdir>
   <categoryname>standard</categoryname>
   <description>scripts that run for run-level 2</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>etc/rc.d/rc3.d</targetdir>
-  <targetdir dist='debian2.2'>etc/rc3.d</targetdir>
+  <targetdir dist='debian'>etc/rc3.d</targetdir>
   <categoryname>standard</categoryname>
   <description>scripts that run for run-level 3</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>etc/rc.d/rc4.d</targetdir>
-  <targetdir dist='debian2.2'>etc/rc4.d</targetdir>
+  <targetdir dist='debian'>etc/rc4.d</targetdir>
   <categoryname>standard</categoryname>
   <description>scripts that run for run-level 4</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>etc/rc.d/rc5.d</targetdir>
-  <targetdir dist='debian2.2'>etc/rc5.d</targetdir>
+  <targetdir dist='debian'>etc/rc5.d</targetdir>
   <categoryname>standard</categoryname>
   <description>scripts that run for run-level 5</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>etc/rc.d/rc6.d</targetdir>
-  <targetdir dist='debian2.2'>etc/rc6.d</targetdir>
+  <targetdir dist='debian'>etc/rc6.d</targetdir>
   <categoryname>standard</categoryname>
   <description>scripts that run for run-level 6</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/lonTabs</targetdir>
   <categoryname>standard</categoryname>
   <description>tab-formatted reference files</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>home/httpd</targetdir>
   <categoryname>standard</categoryname>
   <description>start of the web server tree</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/perl</targetdir>
   <categoryname>server readonly</categoryname>
   <description>perl scripts for managing the LON-CAPA system</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/perl/logs</targetdir>
   <categoryname>server standard</categoryname>
   <description>location where system performance and error logs are kept
   </description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/lon-status/londchld</targetdir>
   <categoryname>server standard</categoryname>
   <description>
@@ -336,91 +345,146 @@ Used by lond parent to check if children
   </description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/perl/tmp</targetdir>
   <categoryname>server standard</categoryname>
   <description>location where temporary files (for caching) are stored
   </description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/prtspool</targetdir>
   <categoryname>server standard</categoryname>
   <description>for the output of lonprintout.pm
   </description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/lib</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>location of LON-CAPA software modules and
+extensions</description>
+</directory>
+<directory dist='default'>
+  <!-- Must protect localauth.pm from extinction. -->
+  <protectionlevel>weak_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/lib/perl</targetdir>
   <categoryname>server readonly</categoryname>
   <description>location of LON-CAPA non web mod-perl handlers</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/lib/perl/Apache</targetdir>
   <categoryname>server readonly</categoryname>
   <description>location of LON-CAPA web mod-perl handlers</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/lib/perl/HTML</targetdir>
   <categoryname>server readonly</categoryname>
   <description>location of HTML specific perl module fixes and additions
   </description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/lib/perl/LONCAPA</targetdir>
   <categoryname>server readonly</categoryname>
   <description>location of HTML specific perl module fixes and additions
   </description>
 </directory>
 <directory dist='default'>
-  <targetdir dist='default'>home/httpd/lonIDs</targetdir>
+   <protectionlevel>modest_delete</protectionlevel>
+ <targetdir dist='default'>home/httpd/lonIDs</targetdir>
   <categoryname>server standard</categoryname>
   <description>cookie jar</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/sockets</targetdir>
   <categoryname>server standard</categoryname>
   <description>lonc's sockets</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/sockets/delayed</targetdir>
   <categoryname>server standard</categoryname>
   <description>lonc's sockets (delayed)</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/cgi-bin</targetdir>
   <categoryname>standard</categoryname>
   <description>location of cgi scripts</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html</targetdir>
   <categoryname>server standard</categoryname>
   <description>location of web-accessible file tree</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/res</targetdir>
   <categoryname>server standard</categoryname>
   <description>root of resource tree</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/userfiles</targetdir>
+  <categoryname>server standard</categoryname>
+  <description>root for user uploaded files</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/adm</targetdir>
   <categoryname>server readonly</categoryname>
   <description>unauthenticated resources</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/adm/rat</targetdir>
   <categoryname>server readonly</categoryname>
   <description>home of the rat</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/adm/help</targetdir>
   <categoryname>server readonly</categoryname>
   <description>online help documentation</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/adm/help/gif</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>online help documentation gif files</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/adm/help/eps</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>online help documentation eps files</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/adm/help/tex</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>online help documentation tex files</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/adm/help/png</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>online help documentation png files</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/adm/help/lib/perl</targetdir>
   <categoryname>server readonly</categoryname>
   <description>online help documentation for the LON-CAPA programming
 interface</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/adm/help/lib/perl/Apache
   </targetdir>
   <categoryname>server readonly</categoryname>
@@ -428,27 +492,32 @@ interface</description>
 interface, Apache (mod_perl) handlers</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/adm/help/scripts</targetdir>
   <categoryname>server readonly</categoryname>
   <description>online help documentation for the LON-CAPA programming
 interface, Apache (mod_perl) handlers</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/adm/lonIcons</targetdir>
   <categoryname>server readonly</categoryname>
   <description>graphic widgets</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/adm/lonMisc</targetdir>
   <categoryname>server readonly</categoryname>
   <description>miscellaneous resources</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/adm/lonKaputt</targetdir>
   <categoryname>server readonly</categoryname>
   <description>error warnings and icons</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/lonUsers</targetdir>
   <categoryname>server standard</categoryname>
   <description>Home directories of local users.  There is a five-tier
@@ -464,79 +533,137 @@ roles.db) which specify the roles and pr
 LON-CAPA system.</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/adm/MathML</targetdir>
   <categoryname>server readonly</categoryname>
   <description>mathematics markup language resources</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/res/adm/includes</targetdir>
   <categoryname>server readonly</categoryname>
   <description>files useful for including within customized scripting
   </description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/res/adm/includes/templates
   </targetdir>
   <categoryname>server readonly</categoryname>
   <description>template files useful for customized scripts</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/lon-status</targetdir>
   <categoryname>server standard</categoryname>
-  <description>status reports</description>
+  <description>status reports; online logs are kept that
+are viewable over the world-wide web</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/res/adm/pages</targetdir>
   <categoryname>server readonly</categoryname>
   <description>web user interface resources</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/adm/lonLCDfont</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>LCD font for remote control</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/adm/lonDomLogos</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>Logos for LON-CAPA domains</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/lonTabs/lonDomColors</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>Designs for LON-CAPA domains</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/adm/lonInterFace</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>Page headers and graphical interface files</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/res/adm/pages/bookmarkmenu
   </targetdir>
   <categoryname>server readonly</categoryname>
   <description>bookmark user interface code</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/res/adm/pages/annotations
   </targetdir>
   <categoryname>server readonly</categoryname>
   <description></description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/res/adm/pages/indexericons
   </targetdir>
   <categoryname>server readonly</categoryname>
   <description>icons that help depict the file system (outdated)</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>usr/lib/perl5/site_perl/5.005</targetdir>
   <targetdir dist='redhat7 redhat7.1'>usr/lib/perl5/site_perl/5.6.0</targetdir>
-  <targetdir dist='debian2.2'>usr/local/lib/perl/5.6.0</targetdir>
+  <targetdir dist='debian'>usr/local/lib/perl/5.6.0</targetdir>
   <categoryname>standard</categoryname>
   <description>system perl tree (usually present on linux systems)
   </description>
 </directory>
 <directory dist='default'>
-  <targetdir dist='default'>usr/local/bin</targetdir>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>usr/local/loncapa/bin</targetdir>
+  <categoryname>standard</categoryname>
+  <description>local binary files for loncapa</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>usr/local/loncapa/doc</targetdir>
+  <categoryname>standard</categoryname>
+  <description>local documentation files for loncapa</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>usr/local/loncapa/doc/conf_examples</targetdir>
+  <categoryname>standard</categoryname>
+  <description>examples of configuration files for secondary
+ services</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>usr/local/loncapa/sbin</targetdir>
   <categoryname>standard</categoryname>
-  <description>local binary files</description>
+  <description>local "auxiliary" binary files for loncapa</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>usr/local/man/man1</targetdir>
   <categoryname>standard</categoryname>
   <description>local manual pages</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>usr/man/man1</targetdir>
   <categoryname>standard</categoryname>
   <description>manual pages</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>usr/man/man3</targetdir>
   <categoryname>standard</categoryname>
   <description>manual pages</description>
 </directory>
 <directory dist='default'>
+  <protectionlevel>never_delete</protectionlevel>
   <targetdir dist='default'>usr/sbin</targetdir>
   <categoryname>standard</categoryname>
   <description>standard linux directory for superuser executables</description>
@@ -545,8 +672,8 @@ LON-CAPA system.</description>
 <files>
 <file>
 <source>loncom/krb.conf</source>
-<target dist='default'>etc/krb.conf</target>
-<categoryname>conf</categoryname>
+<target dist='default'>usr/local/loncapa/doc/conf_examples/krb.conf</target>
+<categoryname>static conf</categoryname>
 <description>
 which Kerberos server to contact for specified Kerberos domains
 </description>
@@ -571,25 +698,23 @@ each list element consists of only two s
 <target dist='default'>etc/httpd/conf/loncapa.conf</target>
 <categoryname>conf</categoryname>
 <description>
+<p>
 The goal of this file is to implement all LON-CAPA specific
-customization of the Apache web server.
-</description>
-</file>
-<file>
-<source>loncom/access.conf</source>
-<target dist='default'>etc/httpd/conf/access.conf</target>
-<categoryname>conf</categoryname>
-<description>
-This file has two major functions.
-For the Apache web server, it defines a global
-access configuration which defines what server options (Indexes", "Includes",
-"FollowSymLinks", "ExecCGI", or "MultiViews") are associated
-with specific directories ("/", "/home/httpd/html", "/home/httpd/cgi-bin",
-and "/usr/doc").  For the LON-CAPA network server and perl module
-handlers, it defines machine specific settings (lonHostID, lonRole,
-lonAdmEMail, lonDefDomain, lonLoadLim, lonExpire, and lonReceipt)
-and internal machine settings for specific directories, socket ports,
-and browser detection logic.
+customization of the Apache web server (most all of these values
+require manual input from the system administrator at some point).
+The values in this file, as opposed to loncapa_apache.conf, are
+meant to be machine and institution specific.
+</p>
+<p>
+For the LON-CAPA network server and perl module
+handlers, it defines machine specific settings including lonHostID, lonRole,
+lonAdmEMail, lonDefDomain, lonLoadLim, lonExpire, and lonReceipt.
+</p>
+<p>
+This file should not be viewable by regular users of the system.
+Only root and www should be able to view the contents of this file
+since lonReceipt is sensitive.
+</p>
 </description>
 <note>
 <b>configure</b>
@@ -611,6 +736,25 @@ MySQL database</td></tr>
 </note>
 </file>
 <file>
+<source>loncom/loncapa_apache.conf</source>
+<target dist='default'>etc/httpd/conf/loncapa_apache.conf</target>
+<categoryname>static conf</categoryname>
+<description>
+The goal of this file is to implement all LON-CAPA specific
+customization of the Apache web server that does not require
+user input.
+
+For the Apache web server, it defines a global
+access configuration which defines what server options (Indexes", "Includes",
+"FollowSymLinks", "ExecCGI", or "MultiViews") are associated
+with specific directories ("/", "/home/httpd/html", "/home/httpd/cgi-bin",
+and "/usr/doc").  For the LON-CAPA network server and perl module
+handlers, it defines 
+and internal machine settings for specific directories, socket ports,
+the www@localhost MySQL password, and browser detection logic.
+</description>
+</file>
+<file>
 <source>loncom/startup.pl</source>
 <target dist='default'>etc/httpd/conf/startup.pl</target>
 <categoryname>static conf</categoryname>
@@ -618,17 +762,22 @@ MySQL database</td></tr>
 This file provides initializations for perl handlers.  It adjusts what
 the module path space is (so as to include /home/httpd/lib/perl/Apache) as
 well as causing the Apache module to be used for every perl handler.
-<tt>startup.pl</tt> is invoked by <tt>access.conf</tt>.
+<tt>startup.pl</tt> is invoked by <tt>loncapa_apache.conf</tt>.
 </description>
 </file>
 <file>
-<source>loncom/publisher/thesaurus.dat</source>
-<target dist='default'>home/httpd/lonTabs/thesaurus.dat</target>
-<categoryname>static conf</categoryname>
+<source>loncom/thesaurus/thesaurus.db</source>
+<target dist='default'>home/httpd/lonTabs/thesaurus.db</target>
+<categoryname>system file</categoryname>
 <description>
-Custom Thesaurus file for LON-CAPA, in the format
-word@wordID@frequency@relatedwordID:frequency,relatedwordID:frequency,...
+Thesaurus database file to be built from loncom/thesaurus/rawkey.txt
 </description>
+<build trigger='run if dependencies change'>
+loncom/thesaurus/build_thesaurus_wrapper.sh
+</build>
+<dependencies>
+rawkey.txt
+</dependencies>
 </file>
 <file>
 <source>loncom/interface/mydesk.tab</source>
@@ -647,8 +796,16 @@ Descriptive list of file extensions, and
 </description>
 </file>
 <file>
-<source>loncom/cgi/barcode.gif</source>
-<target dist='default'>home/httpd/cgi-bin/barcode.gif</target>
+<source>loncom/interface/filecategories.tab</source>
+<target dist='default'>home/httpd/lonTabs/filecategories.tab</target>
+<categoryname>static conf</categoryname>
+<description>
+Descriptive list of file extensions and broad categorization.
+</description>
+</file>
+<file>
+<source>loncom/cgi/barcode.png</source>
+<target dist='default'>home/httpd/cgi-bin/barcode.png</target>
 <categoryname>script</categoryname>
 <description>
 Dynamically outputs a barcode based on a CGI passed encode=BARCODEVALUE
@@ -656,6 +813,14 @@ parameter.
 </description>
 </file>
 <file>
+<source>loncom/cgi/thumbnail.gif</source>
+<target dist='default'>home/httpd/cgi-bin/thumbnail.gif</target>
+<categoryname>script</categoryname>
+<description>
+Produces a thumbnail image of the url given
+</description>
+</file>
+<file>
 <source>loncom/cgi/clusterstatus.pl</source>
 <target dist='default'>home/httpd/cgi-bin/clusterstatus.pl</target>
 <categoryname>script</categoryname>
@@ -664,8 +829,24 @@ utility cgi script to view status of clu
 </description>
 </file>
 <file>
-<source>loncom/cgi/graph.gif</source>
-<target dist='default'>home/httpd/cgi-bin/graph.gif</target>
+<source>loncom/build/system_dependencies/perltest.pl</source>
+<target dist='default'>home/httpd/cgi-bin/perltest.pl</target>
+<categoryname>script</categoryname>
+<description>
+utility cgi script to view status of perl modules
+</description>
+</file>
+<file>
+<source>loncom/build/system_dependencies/cpan_distributions.txt</source>
+<target dist='default'>home/httpd/cgi-bin/cpan_distributions.txt</target>
+<categoryname>interface file</categoryname>
+<description>
+utility cgi script to view status of perl modules
+</description>
+</file>
+<file>
+<source>loncom/cgi/graph.png</source>
+<target dist='default'>home/httpd/cgi-bin/graph.png</target>
 <categoryname>script</categoryname>
 <description>
 Dynamically outputs a graph especially for lonstatistics.pm.
@@ -730,6 +911,16 @@ coil,loop,field,magnetic
 and simply prints this text-only (no markup) to the browser
 </description>
 </file>
+<file>
+<source>loncom/cgi/metadata_harvest.pl</source>
+<target dist='default'>home/httpd/cgi-bin/metadata_harvest.pl</target>
+<categoryname>script</categoryname>
+<description>
+a cgi-script (not mod_perl), which contacts MySQL and pulls
+out all records in "|"-separated format.
+To be used by very simple harvesting engines.
+</description>
+</file>
 <fileglob>
 <glob>*.*</glob>
 <sourcedir>loncom/homework/templates/</sourcedir>
@@ -744,12 +935,16 @@ blank.library;
 blank.library.meta;
 blank.problem;
 blank.problem.meta;
-formula.problem;
-formula.problem.meta;
+Essay.problem;
+Essay.problem.meta;
 numerical.problem;
 numerical.problem.meta;
+Plot.problem;
+Plot.problem.meta;
 RadioResponse.problem;
 RadioResponse.problem.meta;
+RandomLabelExample.problem;
+RandomLabelExample.problem.meta;
 SelectFromOptions-4ConceptGoups.problem;
 SelectFromOptions-4ConceptGoups.problem.meta;
 SelectFromOptions-5ConceptGoups.problem;
@@ -764,8 +959,8 @@ SelectFromOptions-Simple.problem;
 SelectFromOptions-Simple.problem.meta;
 script.library;
 script.library.meta;
-SimpleStringResponse.problem;
-SimpleStringResponse.problem.meta;
+SimpleFormula.problem;
+SimpleFormula.problem.meta;
 StringResponse.problem;
 StringResponse.problem.meta
 </filenames>
@@ -874,9 +1069,8 @@ Basic auth password to access /lon-statu
 </file>
 <file>
 <source>loncom/smb.conf</source>
-<target dist='default'>etc/smb.conf</target>
-<target dist='redhat7 redhat7.1'>etc/samba/smb.conf</target>
-<categoryname>conf</categoryname>
+<target dist='default'>usr/local/loncapa/doc/conf_examples/smb.conf</target>
+<categoryname>static conf</categoryname>
 <description>
 configuration file to make LON-CAPA server file space accessible to network
 neighborhood
@@ -884,8 +1078,8 @@ neighborhood
 </file>
 <file>
 <source>loncom/ntp.conf</source>
-<target dist='default'>etc/ntp.conf</target>
-<categoryname>conf</categoryname>
+<target dist='default'>usr/local/loncapa/doc/conf_examples/ntp.conf</target>
+<categoryname>static conf</categoryname>
 <description>
 which NTP server to contact for information (XNTP3 standard)
 </description>
@@ -909,6 +1103,31 @@ Batch script for updating SQL metadata d
 </description>
 </file>
 <file>
+<source>loncom/metadata_database/cleanup_database.pl</source>
+<target dist='default'>home/httpd/perl/cleanup_database.pl</target>
+<categoryname>script</categoryname>
+<description>
+Batch script for removing temporary tables from the SQL metadata database.
+</description>
+</file>
+<file>
+<source>loncom/misc/cleanup_prtspool.pl</source>
+<target dist='default'>home/httpd/perl/cleanup_prtspool.pl</target>
+<categoryname>script</categoryname>
+<description>
+Batch script for removing files not accessed within 24 hours from the 
+/home/httpd/prtspool directory.
+</description>
+</file>
+<file>
+<source>loncom/lonhttpd</source>
+<target dist='default'>home/httpd/perl/lonhttpd</target>
+<categoryname>script</categoryname>
+<description>
+Small fry httpd on port 8080
+</description>
+</file>
+<file>
 <source>loncom/lonc</source>
 <target dist='default'>home/httpd/perl/lonc</target>
 <categoryname>script</categoryname>
@@ -991,6 +1210,12 @@ echo 'pod2html lond'
 </dependencies>
 </file>
 <file>
+<source>loncom/build/CHECKRPMS</source>
+<target dist='default'>home/httpd/cgi-bin/CHECKRPMS</target>
+<categoryname>script</categoryname>
+<description>CGI script that checks status of RPMs</description>
+</file>
+<file>
 <source>loncom/cgi/loncron.pl</source>
 <target dist='default'>home/httpd/cgi-bin/loncron.pl</target>
 <categoryname>script</categoryname>
@@ -1070,7 +1295,7 @@ new user.
 <target dist='default'>home/httpd/perl/lchtmldir</target>
 <categoryname>setuid script</categoryname>
 <description>
-Manages the file system rammifications of adding author mode to a user. 
+Manages the file system ramifications of adding author mode to a user. 
 If necessary a public_html diretory is added, permissions and ownership are
 set according to the user's authentication mode.
 </description>
@@ -1115,6 +1340,22 @@ GNU General Public License.  Long live t
 </description>
 </file>
 <file>
+<source>loncom/license/httpi.license</source>
+<target dist='default'>home/httpd/html/adm/httpi.license</target>
+<categoryname>interface file</categoryname>
+<description>
+HTTPi webserver license
+</description>
+</file>
+<file>
+<source>loncom/license/httpi.readme</source>
+<target dist='default'>home/httpd/html/adm/httpi.readme</target>
+<categoryname>interface file</categoryname>
+<description>
+HTTPi webserver readme 
+</description>
+</file>
+<file>
 <source>loncom/license/about.html</source>
 <target dist='default'>home/httpd/html/adm/about.html</target>
 <categoryname>interface file</categoryname>
@@ -1140,6 +1381,22 @@ Interface file for responding to imprope
 </description>
 </file>
 <file>
+<source>loncom/html/adm/overloaded.txt</source>
+<target dist='default'>home/httpd/html/adm/overloaded.txt</target>
+<categoryname>interface file</categoryname>
+<description>
+Interface file for responding to overload situations.
+</description>
+</file>
+<file>
+<source>loncom/html/adm/loginproblems.html</source>
+<target dist='default'>home/httpd/html/adm/loginproblems.html</target>
+<categoryname>interface file</categoryname>
+<description>
+Help page for login problems.
+</description>
+</file>
+<file>
 <source>loncom/xml/physnet.sty</source>
 <target dist='default'>home/httpd/html/res/adm/includes/physnet.sty</target>
 <categoryname>static conf</categoryname>
@@ -1157,7 +1414,7 @@ The relevant conditions and metadata to
 </description>
 </file>
 <file>
-<source>loncom/misc/un_keyword.tab</source>
+<source>loncom/thesaurus/un_keyword.tab</source>
 <target dist='default'>home/httpd/html/res/adm/includes/un_keyword.tab</target>
 <categoryname>conf</categoryname>
 <description>
@@ -1211,6 +1468,87 @@ Edit handler for rat maps; TeX content h
 <status>works/unverified</status>
 </file>
 <file>
+<source>loncom/interface/londocs.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/londocs.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler for course documents
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/lonchat.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonchat.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler for chat
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/lonchatfetch.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonchatfetch.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler for periodically fetch new lines of chat
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/lonannounce.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonannounce.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler to put up announcements and calendar
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/lonsyllabus.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonsyllabus.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler to put up syllabus
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/lonsimplepage.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonsimplepage.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler to put up simple page
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/lonpickstudent.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonpickstudent.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler to pick a student from classlist
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/lonbulletin.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonbulletin.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler to put up bulletin board
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/lonaboutme.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonaboutme.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler to put up personal info
+</description>
+<status>works/unverified</status>
+</file>
+<file>
 <source>loncom/publisher/loncfile.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/loncfile.pm</target>
 <categoryname>handler</categoryname>
@@ -1221,6 +1559,396 @@ construction space menu.
 <status>works/unverified</status>
 </file>
 <file>
+<source>loncom/interface/lonhelp.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonhelp.pm</target>
+<categoryname>handler</categoryname>
+<description>
+The .tex file help handler.
+</description>
+<status>works/unverified</status>
+<build trigger='always run'>
+loncom/html/adm/help/buildMakeWrapper
+</build>
+<dependencies>
+Makefile;
+buildMakeWrapper
+</dependencies>
+</file>
+<file>
+<source>loncom/html/adm/help/abouthelp.html</source>
+<target dist='default'>home/httpd/html/adm/help/abouthelp.html</target>
+<categoryname>interface file</categoryname>
+<description>
+Index file for the help system
+</description>
+</file>
+<file>
+<source>doc/help/author.manual.access.tex</source>
+<target dist='default'>home/httpd/html/adm/help/tex/author.manual.access.tex
+</target>
+<categoryname>interface file</categoryname>
+<description>
+The pseudo-LaTeX file to allow people to read the author's manual online, with
+a somewhat clumsy interface.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>doc/help/course.manual.access.tex</source>
+<target dist='default'>home/httpd/html/adm/help/tex/course.manual.access.tex
+</target>
+<categoryname>interface file</categoryname>
+<description>
+The pseudo-LaTeX file to allow people to read the course administrator's
+manual online, with a somewhat clumsy interface.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>doc/help/course.instructor.access.tex</source>
+<target dist='default'>home/httpd/html/adm/help/tex/course.instructor.access.tex
+</target>
+<categoryname>interface file</categoryname>
+<description>
+The pseudo-LaTeX file to allow people to read the course instructor's
+manual online, with a somewhat clumsy interface.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>doc/help/author.manual.ps</source>
+<target dist='default'>home/httpd/html/adm/help/author.manual.ps</target>
+<categoryname>interface file</categoryname>
+<description>
+The postscript Author's Manual
+</description>
+<status>works/unverified</status>
+<dependencies>
+doc/help/author.manual.texxml;
+doc/help/latexSplitter.py;
+doc/help/rebuildLabelHash.pl;
+doc/help/render.texxml.pl;
+doc/help/simpleEdit.py;
+doc/help/texxml2indextex.pl;
+doc/help/texxml2latex.pl;
+loncom/build/buildHelp.sh;
+loncom/build/help_graphics_converter.pl
+</dependencies>
+</file>
+<file>
+<source>doc/help/author.manual.pdf</source>
+<target dist='default'>home/httpd/html/adm/help/author.manual.pdf</target>
+<categoryname>handler</categoryname>
+<description>
+The PDF Author's Manual
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>doc/help/course.manual.ps</source>
+<target dist='default'>home/httpd/html/adm/help/course.manual.ps</target>
+<categoryname>interface file</categoryname>
+<description>
+The postscript Course Manual
+</description>
+<status>works/unverified</status>
+<dependencies>
+doc/help/course.manual.texxml;
+doc/help/latexSplitter.py;
+doc/help/rebuildLabelHash.pl;
+doc/help/render.texxml.pl;
+doc/help/simpleEdit.py;
+doc/help/texxml2indextex.pl;
+doc/help/texxml2latex.pl;
+loncom/build/buildHelp.sh;
+loncom/build/help_graphics_converter.pl
+</dependencies>
+</file>
+<file>
+<source>doc/help/course.manual.pdf</source>
+<target dist='default'>home/httpd/html/adm/help/course.manual.pdf</target>
+<categoryname>interface file</categoryname>
+<description>
+The PDF Course Manual
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>doc/help/course.instructor.ps</source>
+<target dist='default'>home/httpd/html/adm/help/course.instructor.ps</target>
+<categoryname>interface file</categoryname>
+<description>
+The postscript Course Instructor Manual
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>doc/help/course.instructor.pdf</source>
+<target dist='default'>home/httpd/html/adm/help/course.instructor.pdf</target>
+<categoryname>interface file</categoryname>
+<description>
+The PDF Course Instructor Manual
+</description>
+<status>works/unverified</status>
+</file>
+<fileglob>
+<glob>*.*</glob>
+<sourcedir>loncom/html/adm/help/gif/</sourcedir>
+<targetdir dist='default'>
+home/httpd/html/adm/help/gif/</targetdir>
+<categoryname>interface file</categoryname>
+<description>
+Gif files for the help system
+</description>
+<filenames>
+authorRemote.gif;
+constructionSpace.gif;
+constructionSpaceForPublishing.gif;
+creatingANewCourse.gif;
+creatingNewProblemResource.gif;
+dynamic_piecewise.gif;
+dynamic_piecewise2.gif;
+dynamic_plot.gif;
+dynamic_plot2.gif;
+formulaResponse.gif;
+login.gif;
+lonhelpheader.gif;
+mainCourseDocuments.gif;
+mapAdvancedEditorNew.gif;
+mapClickedStart.gif;
+mapEditFirstClick.gif;
+mapEditInitial.gif;
+mapEditingButton.gif;
+mapEditorDirectoryBrowser.gif;
+mapEditorResourceChosen.gif;
+mapEditorSelection.gif;
+mapInsertResource.gif;
+mapNewResource.gif;
+mapSecondWindowSecondResource.gif;
+mapSimpleEditor.gif;
+mapStraightened.gif;
+mapTwoResources.gif;
+numericalResponse1.gif;
+numericalResponseEditor.gif;
+numericalResponseSlopeProblem.gif;
+numericalResponseVarInText.gif;
+optionResponseEditing.gif;
+optionResponseProblem.gif;
+publishMetadata.gif;
+radioResponse2.gif;
+radioResponseHint.gif;
+smallHelp.gif;
+spreadsheet_hierarchy.gif;
+stringResponseEditor.gif;
+studentInterface.gif
+</filenames>
+</fileglob>
+<fileglob>
+<glob>*.*</glob>
+<sourcedir>loncom/html/adm/help/eps/</sourcedir>
+<targetdir dist='default'>
+home/httpd/html/adm/help/eps/</targetdir>
+<categoryname>interface file</categoryname>
+<description>
+EPS files for the help system
+</description>
+<filenames>
+authorRemote.eps;
+constructionSpace.eps;
+constructionSpaceForPublishing.eps;
+creatingANewCourse.eps;
+creatingNewProblemResource.eps;
+dynamic_piecewise.eps;
+dynamic_piecewise2.eps;
+dynamic_plot.eps;
+dynamic_plot2.eps;
+formulaResponse.eps;
+lonhelpheader.eps;
+login.eps;
+mainCourseDocuments.eps;
+mapAdvancedEditorNew.eps;
+mapClickedStart.eps;
+mapEditFirstClick.eps;
+mapEditInitial.eps;
+mapEditingButton.eps;
+mapEditorDirectoryBrowser.eps;
+mapEditorResourceChosen.eps;
+mapEditorSelection.eps;
+mapInsertResource.eps;
+mapNewResource.eps;
+mapSecondWindowSecondResource.eps;
+mapSimpleEditor.eps;
+mapStraightened.eps;
+mapTwoResources.eps;
+numericalResponse1.eps;
+numericalResponseEditor.eps;
+numericalResponseSlopeProblem.eps;
+numericalResponseVarInText.eps;
+optionResponseEditing.eps;
+optionResponseProblem.eps;
+publishMetadata.eps;
+radioResponse2.eps;
+radioResponseHint.eps;
+smallHelp.eps;
+spreadsheet_hierarchy.eps;
+stringResponseEditor.eps;
+studentInterface.eps
+</filenames>
+</fileglob>
+<fileglob>
+<glob>*.*</glob>
+<sourcedir>loncom/html/adm/help/tex/</sourcedir>
+<targetdir dist='default'>
+home/httpd/html/adm/help/tex/</targetdir>
+<categoryname>interface file</categoryname>
+<description>
+Tex files for the help system
+</description>
+<filenames>
+About_Authors_Manual.tex;
+About_Numerical_and_Formula_Response.tex;
+Ambiguous_Reference.tex;
+Author_LON-CAPA_Introduction.tex;
+Author_Manual_Title_Page.tex;
+Author_Numerical_and_Formula.tex;
+Author_Remote_Control.tex;
+Authoring_Adding_Pictures.tex;
+Authoring_Dynamic_Plot.tex;
+Authoring_HTML_vs_Tex.tex;
+Authoring_M_Tag.tex;
+Authoring_Piecewise_Plot.tex;
+Calling_Functions.tex;
+Coauthor.tex;
+Construction_Space_Overview.tex;
+Course_Add_Student.tex;
+Course_Chart_To_Excel.tex;
+Course_Convert_To_CSV.tex;
+Course_Create_Class_List.tex;
+Course_Critical_Message.tex;
+Course_Deleting.tex;
+Course_Disable_Discussion.tex;
+Course_Discussion_Board.tex;
+Course_Drop_Student.tex;
+Course_Edit_Content.tex;
+Course_Feedback_Addresses.tex;
+Course_Homework_Performance_Overview.tex;
+Course_Manual_Title_Page.tex;
+Course_Message_Access.tex;
+Course_Problem_Weight.tex;
+Course_Setting_Parameters.tex;
+Course_Student_Grade_Override.tex;
+Course_Student_Work.tex;
+Course_Toplevel_Seq.tex;
+Creating_A_Course_Intro.tex;
+Creating_New_Content_Pages.tex;
+Creating_Online_Problems.tex;
+Creating_Radio_Response_Problems.tex;
+Docs_Adding_Course_Doc.tex;
+Docs_Adding_External_Resource.tex;
+Docs_Adding_Folders.tex;
+Docs_Creating_From_Template.tex;
+Docs_Importing_LON-CAPA_Resource.tex;
+Docs_Main_Course_Documents.tex;
+Docs_Navigate_Content.tex;
+Docs_Overview.tex;
+Docs_Supplemental.tex;
+Docs_Uploading_From_Harddrive.tex;
+Foils.tex;
+Formula_Response_Example.tex;
+Formula_Response_Limitations.tex;
+Formula_Response_Problems.tex;
+Formula_Response_Sampling.tex;
+Formula_Tolerance.tex;
+General_Intro.tex;
+How_To_Edit_Existing_Content_Pages.tex;
+Latex_Footer.tex;
+Latex_Header.tex;
+Login_To_LON-CAPA.tex;
+Metadata_Description.tex;
+Navmap_Host_Down.tex;
+Numerical_Response_Advanced_Example.tex;
+Numerical_Response_Format.tex;
+Numerical_Response_Intro.tex;
+Numerical_Response_Introduction.tex;
+Numerical_Response_Parts_A.tex;
+Numerical_Response_Parts_B.tex;
+Numerical_Response_Problems.tex;
+Numerical_Response_Randomization.tex;
+Numerical_Response_Simple_Example.tex;
+Numerical_Response_Tutorial_A.tex;
+Numerical_Response_Units.tex;
+Option_Response_Concept_Group_Example.tex;
+Option_Response_Matching_Example.tex;
+Option_Response_Problem_Creation.tex;
+Option_Response_Problem_Figure.tex;
+Option_Response_Problem_Parts.tex;
+Option_Response_Problems.tex;
+Option_Response_Simple.tex;
+Part_Tag_Edit_Help.tex;
+Problem_Editor_Testing_Area.tex;
+Problem_Editor_XML_Index.tex;
+Problem_Types.tex;
+Publishing_A_Resource.tex;
+Publishing_Author_Tutorial_Segue.tex;
+Publishing_Copyright.tex;
+Publishing_Intro.tex;
+Publishing_Keywords.tex;
+Quick_Grades_Possibly_Correct.tex;
+Radio_Response_Problems.tex;
+Radio_Response_Randomization.tex;
+Resource_Types.tex;
+Script_Tutorial_Intro.tex;
+Scripting_Help.tex;
+Sequence_Advanced_Editor_Creation.tex;
+Sequence_Definition.tex;
+Sequence_Editor_Selection.tex;
+Sequence_Page_Maps.tex;
+Sequence_Simple_Editor_Creation.tex;
+Sequence_Top-Level.tex;
+Significant_Figures.tex;
+Spreadsheet_About.tex;
+Spreadsheet_Alternative_View.tex;
+Spreadsheet_Changes_To_Grading.tex;
+Spreadsheet_Col_Sum.tex;
+Spreadsheet_Completely_Recalc.tex;
+Spreadsheet_Empty_Rows.tex;
+Spreadsheet_Export_Row.tex;
+Spreadsheet_Functions.tex;
+Spreadsheet_Import_Values.tex;
+Spreadsheet_Levels.tex;
+Spreadsheet_Lists.tex;
+Spreadsheet_Max_Depth_Exceeded.tex;
+Spreadsheet_OOO_Rows.tex;
+Spreadsheet_Op_On_All_Problem_Parts.tex;
+Spreadsheet_Parms.tex;
+Spreadsheet_Problem_Weight.tex;
+Spreadsheet_Ranges.tex;
+Spreadsheet_Specifying_Cells.tex;
+Spreadsheet_Student_Visible.tex;
+Spreadsheet_Symbolic_Names.tex;
+Spreadsheet_Template_Row.tex;
+Spreadsheet_Ternary_Operator.tex;
+Spreadsheet_Tries.tex;
+String_Response_Problem_Creation.tex;
+String_Response_Problems.tex;
+Tolerance.tex;
+Variable_Naming_Conventions.tex;
+Variable_Tutorial_A.tex;
+Variables_in_Scripts.tex;
+Variables_in_the_Answer_Block.tex;
+Variables_in_the_Text_Block.tex
+</filenames>
+</fileglob>
+<file>
+<source>loncom/html/adm/help/fragmentLabels.gdbm</source>
+<target dist='default'>home/httpd/html/adm/help/fragmentLabels.gdbm</target>
+<categoryname>interface file</categoryname>
+<description>
+A gdbm file containing a label->tex file hash.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
 <source>loncom/interface/lonstatistics.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/lonstatistics.pm</target>
 <categoryname>handler</categoryname>
@@ -1230,6 +1958,46 @@ Handler to show statistics on solving LO
 <status>works/unverified</status>
 </file>
 <file>
+<source>loncom/interface/statistics/lonproblemstatistics.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonproblemstatistics.pm
+</target>
+<categoryname>handler</categoryname>
+<description>
+The module that generate the html for the Problem Statistics web pages.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/statistics/lonpercentage.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonpercentage.pm
+</target>
+<categoryname>handler</categoryname>
+<description>
+The module that generate the html for the Percentage graph web pages.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/statistics/lonproblemanalysis.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonproblemanalysis.pm
+</target>
+<categoryname>handler</categoryname>
+<description>
+The module that generate the html for the Problem Analysis web pages.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/interface/statistics/lonstudentassessment.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonstudentassessment.pm
+</target>
+<categoryname>handler</categoryname>
+<description>
+The module that generate the html for the Student Assessment/Chart web pages.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
 <source>loncom/publisher/londiff.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/londiff.pm</target>
 <categoryname>handler</categoryname>
@@ -1300,7 +2068,8 @@ Handler to evaluate externally graded re
 <target dist='default'>home/httpd/lib/perl/Apache/loncapagrade.pm</target>
 <categoryname>handler</categoryname>
 <description>
-Handler to evaluate externally graded responses.
+Holds results and defines
+tag handlers needed by externalresponse.pm
 </description>
 <status>works/unverified</status>
 </file>
@@ -1313,6 +2082,14 @@ Handler to publish directories.
 </description>
 </file>
 <file>
+<source>loncom/publisher/lonunauthorized.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonunauthorized.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler to explain failed contruction space access.
+</description>
+</file>
+<file>
 <source>doc/man/Apache__lonpubdir.3</source>
 <target dist='default'>usr/man/man3/Apache::lonpubdir.3</target>
 <categoryname>doc</categoryname>
@@ -1475,11 +2252,19 @@ them roles.
 <status>works/unverified</status>
 </file>
 <file>
-<source>loncom/interface/lonchart.pm</source>
-<target dist='default'>home/httpd/lib/perl/Apache/lonchart.pm</target>
+<source>loncom/interface/lonhtmlcommon.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonhtmlcommon.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Contains a set of functions that generate html controls and data layouts
+</description>
+</file>
+<file>
+<source>loncom/interface/loncoursedata.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/loncoursedata.pm</target>
 <categoryname>handler</categoryname>
 <description>
-Produces simple LectureOnline-like student assessment performance chart
+Common functions for handling student course data (download and process)
 </description>
 </file>
 <file>
@@ -1632,6 +2417,15 @@ Handles navigational maps.
 <status>works/unverified</status>
 </file>
 <file>
+<source>loncom/interface/lonquickgrades.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonquickgrades.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Student quick grades interface.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
 <source>loncom/interface/lonpreferences.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/lonpreferences.pm</target>
 <categoryname>handler</categoryname>
@@ -1660,6 +2454,15 @@ Handles a searchable catalogue.
 <status>works/unverified</status>
 </file>
 <file>
+<source>loncom/interface/lonmysql.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonmysql.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Provides utility functions for creating and accessing mysql database tables.
+</description>
+<status>works/unverified</status>
+</file>
+<file>
 <source>doc/man/Apache__lonsearchcat.3</source>
 <target dist='default'>usr/man/man3/Apache::lonsearchcat.3</target>
 <categoryname>doc</categoryname>
@@ -1861,6 +2664,15 @@ Homework remote control.
 <status>works/unverified</status>
 </file>
 <file>
+<source>loncom/html/res/adm/pages/chatroom.html</source>
+<target dist='default'>home/httpd/html/res/adm/pages/chatroom.html</target>
+<categoryname>handler</categoryname>
+<description>
+Establishes frameset for chatroom
+</description>
+<status>works/unverified</status>
+</file>
+<file>
 <source>loncom/html/res/adm/pages/annotator/admannotations.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/admannotations.pm</target>
 <categoryname>handler</categoryname>
@@ -1933,7 +2745,7 @@ loncom/build/pod2html.sh ../../rat/lonpa
 <target dist='default'>home/httpd/lib/perl/Apache/lonuserstate.pm</target>
 <categoryname>handler</categoryname>
 <description>
-compile course into binary data structure (in loncom/rat)
+compile course into binary data structure
 </description>
 <status>works/unverified</status>
 </file>
@@ -1973,7 +2785,7 @@ echo 'pod2html lonuserstate.pm'
 <target dist='default'>home/httpd/lib/perl/Apache/lontex.pm</target>
 <categoryname>handler</categoryname>
 <description>
-Handler for tex files (somewhere in modules)
+Handler for tex files
 </description>
 <status>works/unverified</status>
 </file>
@@ -2042,6 +2854,30 @@ implements &lt;script&gt;, &lt;scriptlib
 <status>works/unverified</status>
 </file>
 <file>
+<source>loncom/homework/randomlylabel.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/randomlylabel.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler for compositing images, and text together.
+</description>
+</file>
+<file>
+<source>loncom/homework/rankresponse.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/rankresponse.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler for rankresponse
+</description>
+</file>
+<file>
+<source>loncom/homework/matchresponse.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/matchresponse.pm</target>
+<categoryname>handler</categoryname>
+<description>
+Handler for matchresponse
+</description>
+</file>
+<file>
 <source>loncom/homework/randomlabel.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/randomlabel.pm</target>
 <categoryname>handler</categoryname>
@@ -2110,10 +2946,12 @@ a way that does not threaten the operati
 </file>
 <file>
 <source>loncom/auth/localauth.pm</source>
-<target dist='default'>home/httpd/lib/perl/localauth.pm</target>
+<target dist='default'>home/httpd/lib/perl/localauth-std.pm</target>
 <categoryname>handler</categoryname>
 <description>
-Local authentication mechanism (meant to be customized).
+Local authentication mechanism.  The target file is meant as a template
+for a localauth.pm file.  The target file with the -std suffix is not
+used directly by any software program; it is just a template file.
 </description>
 <status>works/unverified</status>
 </file>
@@ -2168,6 +3006,34 @@ access handler for file transfers
 <status>works/unverified</status>
 </file>
 <file>
+<source>loncom/auth/lontokacc.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lontokacc.pm</target>
+<categoryname>handler</categoryname>
+<description>
+handler for inter-server transfer of token accessed files, includes
+cleanup handler to remove file when successfully done
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/auth/lonuploadedacc.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lonuploadedacc.pm</target>
+<categoryname>handler</categoryname>
+<description>
+access handler for user uploaded files
+</description>
+<status>works/unverified</status>
+</file>
+<file>
+<source>loncom/lontrans.pm</source>
+<target dist='default'>home/httpd/lib/perl/Apache/lontrans.pm</target>
+<categoryname>handler</categoryname>
+<description>
+URI to filename translation
+</description>
+<status>works/unverified</status>
+</file>
+<file>
 <source>doc/man/Apache__lonracc.3</source>
 <target dist='default'>usr/man/man3/Apache::lonracc.3</target>
 <categoryname>doc</categoryname>
@@ -2415,6 +3281,12 @@ loncom/build/pod2html.sh ../lonnet/perl/
 <categoryname>interface file</categoryname>
 <description>bumps to login</description>
 </file>
+<file>
+<source>loncom/html/favicon.ico</source>
+<target dist='default'>home/httpd/html/favicon.ico</target>
+<categoryname>interface file</categoryname>
+<description>Bookmark and tab icon</description>
+</file>
 <link>
 <linkto>etc/mime.types</linkto>
 <target dist='default'>etc/httpd/conf/mime.types</target>
@@ -2478,6 +3350,22 @@ javascript
 </description>
 </file>
 <file>
+<source>rat/client/extpickcode.html</source>
+<target dist='default'>home/httpd/html/adm/rat/extpickcode.html</target>
+<categoryname>interface file</categoryname>
+<description>
+javascript
+</description>
+</file>
+<file>
+<source>rat/client/extpickframe.html</source>
+<target dist='default'>home/httpd/html/adm/rat/extpickframe.html</target>
+<categoryname>interface file</categoryname>
+<description>
+javascript
+</description>
+</file>
+<file>
 <source>rat/client/map.html</source>
 <target dist='default'>home/httpd/html/adm/rat/map.html</target>
 <categoryname>interface file</categoryname>
@@ -2636,13 +3524,14 @@ lonlogo_broken.mov
 <targetdir dist='default'>home/httpd/html/adm/lonIcons/</targetdir>
 <categoryname>graphic file</categoryname>
 <description>
-logos
+logos and general widget icons
 </description>
 <filenames>
 SMETE_white.gif;
 aboutlon.gif;
 accessbutton.gif;
 arrow_up.gif;
+branch.gif;
 cab.gif;
 cab_big.gif;
 capapanel.gif;
@@ -2694,6 +3583,11 @@ mov.gif;
 mov_big.gif;
 move_up.gif;
 move_down.gif;
+navmap.correct.gif;
+navmap.open.gif;
+navmap.wrong.gif;
+navmap.folder.open.gif;
+navmap.folder.closed.gif;
 page.gif;
 page_big.gif;
 pdf.gif;
@@ -2721,6 +3615,7 @@ survey.gif;
 survey_big.gif;
 tex.gif;
 tex_big.gif;
+tth.gif;
 txt.gif;
 txt_big.gif;
 unknown.gif;
@@ -2755,9 +3650,7 @@ zip_big.gif
 <targetdir dist='default'>home/httpd/html/adm/lonMisc/</targetdir>
 <categoryname>graphic file</categoryname>
 <description>
-Miscellaneous resources.  Respectively: button for catalog,
-button to set parameters in a page,
-button to do regrades, button to check on problem submissions,
+Miscellaneous resources.
 </description>
 <filenames>
 authorfeed.gif;
@@ -2805,7 +3698,6 @@ tested
 Configuration file reader (looks in /etc/httpd/conf/); accepts
 a list of *.conf files to inspect for PerlSetVar key/value
 entries.
-tested
 </description>
 <status>works/unverified</status>
 </file>
@@ -2995,19 +3887,134 @@ Define unit prefixing and conversion for
 </description>
 </file>
 <fileglob>
+<glob>*.jpg</glob>
+<sourcedir>loncom/html/adm/lonInterFace/</sourcedir>
+<targetdir dist='default'>home/httpd/html/adm/lonInterFace/</targetdir>
+<categoryname>graphic file</categoryname>
+<description>Pages headers</description>
+<filenames>
+admin.jpg;
+author.jpg;
+coordinator.jpg;
+header.jpg;
+student.jpg;
+</filenames>
+</fileglob>
+<fileglob>
+<glob>*.gif</glob>
+<sourcedir>loncom/html/adm/lonDomLogos/</sourcedir>
+<targetdir dist='default'>home/httpd/html/adm/lonDomLogos/</targetdir>
+<categoryname>graphic file</categoryname>
+<description>Logos of LON-CAPA domains</description>
+<filenames>
+103.gif;
+gerd.gif;
+mio.gif;
+msuvu.gif;
+ohiou.gif;
+rhs.gif;
+sfu.gif;
+tmcc.gif;
+umich.gif;
+worf.gif;
+annarbor.gif;
+elps.gif;
+gwu.gif;
+msudemo.gif;
+ndsu.gif;
+physnet.gif;
+sc.gif;
+Selwyn.gif;
+ucf.gif;
+unihalle.gif;
+wscc.gif;
+cps.gif;
+fsu.gif;
+lsd.gif;
+msu.gif;
+nsdl.gif;
+pmm.gif;
+sunysb.gif;
+udel.gif;
+uz.gif
+</filenames>
+</fileglob>
+<fileglob>
+<glob>*.tab</glob>
+<sourcedir>loncom/html/adm/lonDomColors/</sourcedir>
+<targetdir dist='default'>home/httpd/lonTabs/lonDomColors/</targetdir>
+<categoryname>conf</categoryname>
+<description>Designs of LON-CAPA domains</description>
+<filenames>
+annarbor.tab;
+default.tab;
+msu.tab;
+sfu.tab;
+worf.tab
+</filenames>
+</fileglob>
+<fileglob>
+<glob>*.gif</glob>
+<sourcedir>loncom/html/adm/lonLCDfont/</sourcedir>
+<targetdir dist='default'>home/httpd/html/adm/lonLCDfont/</targetdir>
+<categoryname>graphic file</categoryname>
+<description>LON-CAPA remote control LCD font</description>
+<filenames>
+0.gif;
+1.gif;
+2.gif;
+3.gif;
+4.gif;
+5.gif;
+6.gif;
+7.gif;
+8.gif;
+9.gif;
+a.gif;
+b.gif;
+c.gif;
+d.gif;
+e.gif;
+f.gif;
+g.gif;
+h.gif;
+i.gif;
+j.gif;
+k.gif;
+l.gif;
+m.gif;
+n.gif;
+o.gif;
+p.gif;
+q.gif;
+r.gif;
+s.gif;
+t.gif;
+u.gif;
+v.gif;
+w.gif;
+x.gif;
+y.gif;
+z.gif;
+colon.gif;
+hyphen.gif;
+slash.gif;
+space.gif;
+</filenames>
+</fileglob>
+<fileglob>
 <glob>*.gif</glob>
 <sourcedir>loncom/html/res/adm/pages/</sourcedir>
 <targetdir dist='default'>home/httpd/html/res/adm/pages/</targetdir>
 <categoryname>graphic file</categoryname>
 <description>icons used for the entire LON-CAPA user interface</description>
 <filenames>
-a.gif;
+anno.gif;
 anot.gif;
-b.gif;
 back.gif;
+bchat.gif;
 bkm.gif;
 brws.gif;
-c.gif;
 catalog.gif;
 ccrs.gif;
 chat.gif;
@@ -3016,71 +4023,48 @@ com.gif;
 courses.gif;
 cprv.gif;
 cstr.gif;
-d.gif;
 dempty.gif;
-e.gif;
+docs.gif;
 egrd.gif;
 empty.gif;
 enrl.gif;
 eval.gif;
-f.gif;
 fdbk.gif;
 feedback.gif;
 forw.gif;
-g.gif;
 grds.gif;
 group.gif;
-h.gif;
 help.gif;
-hyphen.gif;
-i.gif;
 info.gif;
-j.gif;
-k.gif;
-l.gif;
 ledblink.gif;
 ledgreen.gif;
 ledoff.gif;
 ledon.gif;
 ledsend.gif;
 logout.gif;
-m.gif;
 mrk.gif;
-n.gif;
 nav.gif;
 next.gif;
-o.gif;
-p.gif;
+nothumb.gif;
 parm.gif;
 pgrd.gif;
 pparm.gif;
 pref.gif;
 prev.gif;
 prt.gif;
-q.gif;
 qempty.gif;
-r.gif;
 reload.gif;
 remotebg.gif;
 res.gif;
 roles.gif;
-s.gif;
 sbkm.gif;
-space.gif;
 spacer.gif;
 sprs.gif;
 src.gif;
 stat.gif;
 subm.gif;
-t.gif;
 title.gif;
-u.gif;
-v.gif;
 vbkm.gif;
-w.gif;
-x.gif;
-y.gif;
-z.gif
 </filenames>
 </fileglob>
 <file>
@@ -3114,7 +4098,7 @@ renders the HTML (including image maps)
 </targetdir>
 <categoryname>graphic file</categoryname>
 <description>
-icons used for the bookmark portion of the LON-CAPA user interface
+icons used for directory indexing and login screen
 </description>
 <filenames>
 a.gif;
@@ -3215,7 +4199,7 @@ world2.gif
 </targetdir>
 <categoryname>graphic file</categoryname>
 <description>
-icons used for directory indexing and login screen
+icons used for the bookmark portion of the LON-CAPA user interface
 </description>
 <filenames>
 folder_anim.gif;
@@ -3250,7 +4234,7 @@ ur_corner.gif
 </targetdir>
 <categoryname>interface file</categoryname>
 <description>
-associated with the frameset scheme of displaying bookmarks
+associated with the scheme of displaying bookmarks
 </description>
 <filenames>
 bookmarkmenu_toolbar.html;
@@ -3268,9 +4252,18 @@ javascript for handling client-side inte
 </description>
 </file>
 <file>
+<source>loncom/build/CHECKRPMS</source>
+<target dist='default'>usr/local/loncapa/bin/CHECKRPMS</target>
+<categoryname>system script</categoryname>
+<description>
+manilla wrapper around check-rpms
+</description>
+<status>tested/documented/beta</status>
+</file>
+<file>
 <source>loncom/build/check-rpms</source>
-<target dist='default'>usr/local/bin/check-rpms</target>
-<categoryname>root script</categoryname>
+<target dist='default'>usr/local/loncapa/bin/check-rpms</target>
+<categoryname>system script</categoryname>
 <description>
 compare installed rpms with up-to-date distribution
 </description>
@@ -3307,12 +4300,14 @@ loncom/build/pod2html.sh check-rpms &gt;
 </file>
 <file>
 <source>loncom/build/loncaparestoreconfigurations</source>
-<target dist='default'>usr/sbin/loncaparestoreconfigurations</target>
+<target dist='default'>usr/local/loncapa/sbin/loncaparestoreconfigurations
+</target>
 <categoryname>script</categoryname>
 <description>
-restores .rpmsave files after a LON-CAPA-base upgrade
+Updates .lpmlnew files with previous settings.  Also supports alternative
+schemes of settings-updating and file-overwriting.
 </description>
-<status>deprecated</status>
+<status>works/unverified</status>
 </file>
 <file>
 <source>loncom/cron/loncapa</source>
@@ -3324,8 +4319,9 @@ file that specifies periodic processes t
 </file>
 <file>
 <source>loncom/ntp/step-tickers</source>
-<target dist='default'>etc/ntp/step-tickers</target>
-<categoryname>conf</categoryname>
+<target dist='default'>usr/local/loncapa/doc/conf_examples/ntp_step-tickers
+</target>
+<categoryname>static conf</categoryname>
 <description>
 file that stimulates running of ntpdate upon init.d/xntpd initiation
 </description>
@@ -3376,8 +4372,8 @@ symbolic links to /etc/rc.d/init.d/lonco
 </link>
 <file>
 <source>loncom/atalk/config</source>
-<target dist='default'>etc/atalk/config</target>
-<categoryname>conf</categoryname>
+<target dist='default'>usr/local/loncapa/doc/conf_examples/config</target>
+<categoryname>static conf</categoryname>
 <description>
 configuration file to make LON-CAPA server file space accessible to
 Appleshares access (Macintosh)