--- doc/loncapafiles/loncapafiles.lpml	2003/06/02 17:15:58	1.246
+++ doc/loncapafiles/loncapafiles.lpml	2003/07/01 18:27:06	1.258
@@ -2,7 +2,7 @@
  "http://lpml.sourceforge.net/DTD/lpml.dtd">
 <!-- loncapafiles.lpml -->
 
-<!-- $Id: loncapafiles.lpml,v 1.246 2003/06/02 17:15:58 bowersj2 Exp $ -->
+<!-- $Id: loncapafiles.lpml,v 1.258 2003/07/01 18:27:06 albertel Exp $ -->
 
 <!--
 
@@ -459,6 +459,12 @@ extensions</description>
 </directory>
 <directory dist='default'>
   <protectionlevel>modest_delete</protectionlevel>
+  <targetdir dist='default'>home/httpd/html/adm/jme</targetdir>
+  <categoryname>server readonly</categoryname>
+  <description>JME support files</description>
+</directory>
+<directory dist='default'>
+  <protectionlevel>modest_delete</protectionlevel>
   <targetdir dist='default'>home/httpd/html/adm/helper</targetdir>
   <categoryname>server readonly</categoryname>
   <description>XML specifications for helpers</description>
@@ -1015,8 +1021,8 @@ Built from Glabel.java.  Still working o
 </note>
 </file>
 <file>
-<source>loncom/interface/default.assesscalc</source>
-<target dist='default'>home/httpd/html/res/adm/includes/default.assesscalc
+<source>loncom/interface/spreadsheet/default_assesscalc</source>
+<target dist='default'>home/httpd/html/res/adm/includes/default_assesscalc
 </target>
 <categoryname>static conf</categoryname>
 <description>
@@ -1024,8 +1030,8 @@ Default spreadsheet for individual asses
 </description>
 </file>
 <file>
-<source>loncom/interface/default.studentcalc</source>
-<target dist='default'>home/httpd/html/res/adm/includes/default.studentcalc
+<source>loncom/interface/spreadsheet/default_studentcalc</source>
+<target dist='default'>home/httpd/html/res/adm/includes/default_studentcalc
 </target>
 <categoryname>static conf</categoryname>
 <description>
@@ -1033,8 +1039,8 @@ Default spreadsheet for assessment of st
 </description>
 </file>
 <file>
-<source>loncom/interface/default.classcalc</source>
-<target dist='default'>home/httpd/html/res/adm/includes/default.classcalc
+<source>loncom/interface/spreadsheet/default_classcalc</source>
+<target dist='default'>home/httpd/html/res/adm/includes/default_classcalc
 </target>
 <categoryname>static conf</categoryname>
 <description>
@@ -1665,17 +1671,6 @@ manual online, with a somewhat clumsy in
 <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>
@@ -1733,24 +1728,6 @@ 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>
@@ -1868,23 +1845,46 @@ Tex files for the help system
 About_Authors_Manual.tex;
 About_Numerical_and_Formula_Response.tex;
 Ambiguous_Reference.tex;
-Analyze_problem.tex;
+Analyze_Problem.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_DataResponse.tex;
 Authoring_Dynamic_Plot.tex;
+Authoring_ExternalResponse.tex;
+Authoring_Foil_Structure_Tags.tex;
 Authoring_HTML_vs_Tex.tex;
+Authoring_Hint_Tags.tex;
+Authoring_ImageResponse.tex;
+Authoring_Input_Tags.tex;
+Authoring_Internal_Tags.tex;
 Authoring_M_Tag.tex;
+Authoring_NumericalResponse.tex;
+Authoring_OptionResponse.tex;
+Authoring_Output_Tags.tex;
+Authoring_Pictures_EPS.tex;
 Authoring_Piecewise_Plot.tex;
+Authoring_RadiobuttonResponse.tex;
+Authoring_Response_Attributes.tex;
+Authoring_Response_Tag_Intro.tex;
+Authoring_Responseparam_Parameter.tex;
+Authoring_Scripting_Tags.tex;
+Authoring_Structure_Tags.tex;
+Authoring_XML_Intro.tex;
+CAPA_LON-CAPA_function_diffs.tex;
 Calendar_Add_Announcement.tex;
 Calendar_Remove_Announcement.tex;
 Calling_Functions.tex;
+Chart_Description.tex;
+Chart_Output_Data.tex;
+Chart_Output_Formats.tex;
 Coauthor.tex;
 Construction_Space_Overview.tex;
 Course_Add_Student.tex;
 Course_Chart_To_Excel.tex;
+Course_Chat.tex;
 Course_Convert_To_CSV.tex;
 Course_Create_Class_List.tex;
 Course_Critical_Message.tex;
@@ -1893,15 +1893,20 @@ Course_Disable_Discussion.tex;
 Course_Discussion_Board.tex;
 Course_Drop_Student.tex;
 Course_Edit_Content.tex;
+Course_Face_To_Face_Records.tex;
 Course_Feedback_Addresses.tex;
 Course_Homework_Performance_Overview.tex;
 Course_Manual_Title_Page.tex;
 Course_Message_Access.tex;
+Course_Modify_Student_Data.tex;
 Course_Problem_Weight.tex;
+Course_Set_Start_End_Date.tex;
 Course_Setting_Parameters.tex;
 Course_Student_Grade_Override.tex;
 Course_Student_Work.tex;
 Course_Toplevel_Seq.tex;
+Course_User_Evaluation.tex;
+Create_Course.tex;
 Creating_A_Course_Intro.tex;
 Creating_New_Content_Pages.tex;
 Creating_Online_Problems.tex;
@@ -1917,10 +1922,10 @@ Docs_Overview.tex;
 Docs_Supplemental.tex;
 Docs_Uploading_From_Harddrive.tex;
 Foils.tex;
+Formula_Response_Adv_Intro.tex;
 Formula_Response_Example.tex;
 Formula_Response_Limitations.tex;
 Formula_Response_Problems.tex;
-Formula_Response_Adv_Intro.tex;
 Formula_Response_Sampling.tex;
 Formula_Tolerance.tex;
 General_Intro.tex;
@@ -1928,6 +1933,7 @@ Greek_Symbols.tex;
 How_To_Edit_Existing_Content_Pages.tex;
 Latex_Footer.tex;
 Latex_Header.tex;
+Leaving_Feedback.tex;
 Login_To_LON-CAPA.tex;
 Metadata_Description.tex;
 Navmap_Host_Down.tex;
@@ -1951,8 +1957,12 @@ Option_Response_Problems.tex;
 Option_Response_Simple.tex;
 Other_Symbols.tex;
 Part_Tag_Edit_Help.tex;
+Physical_Units.tex;
+Prefs_Forwarding.tex;
+Prefs_Screen_Name_Nickname.tex;
 Problem_Editor_Testing_Area.tex;
 Problem_Editor_XML_Index.tex;
+Problem_LON-CAPA_Functions.tex;
 Problem_Types.tex;
 Publishing_A_Resource.tex;
 Publishing_Author_Tutorial_Segue.tex;
@@ -1962,8 +1972,11 @@ Publishing_Keywords.tex;
 Quick_Grades_Possibly_Correct.tex;
 Radio_Response_Problems.tex;
 Radio_Response_Randomization.tex;
+Ranking_Problems.tex;
 Resource_Types.tex;
+Script_Functions.tex;
 Script_Tutorial_Intro.tex;
+Script_Variables.tex;
 Scripting_Help.tex;
 Sequence_Advanced_Editor_Creation.tex;
 Sequence_Definition.tex;
@@ -1997,12 +2010,17 @@ Spreadsheet_Ternary_Operator.tex;
 Spreadsheet_Tries.tex;
 String_Response_Problem_Creation.tex;
 String_Response_Problems.tex;
+Syllabus_ExtLink.tex;
+Syllabus_URLs.tex;
 Tolerance.tex;
+Uploaded_Templates_PublicView.tex;
+Uploaded_Templates_TextBoxes.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
+Variables_in_the_Text_Block.tex;
+all_functions_table.tex;
 </filenames>
 </fileglob>
 <file>
@@ -2414,6 +2432,33 @@ assignment.
 </description>
 <status>works/unverified</status>
 </file>
+
+<file>
+  <source>loncom/homework/chemresponse.pm</source>
+  <target dist='default'>home/httpd/lib/perl/Apache/chemresponse.pm</target>
+  <categoryname>handler</categoryname>
+  <description>
+    Handle the tags organicresponse/structure and reationresponse
+  </description>
+  <status>works/unverified</status>
+</file>
+
+<fileglob>
+  <glob>*.*</glob>
+  <sourcedir>loncom/html/adm/jme/</sourcedir>
+  <targetdir dist='default'>home/httpd/html/adm/jme/</targetdir>
+  <categoryname>interface file</categoryname>
+  <description>
+    JME files, for editing organic structures
+  </description>
+  <filenames>
+JME.jar;
+jme.gif;
+jme_help.html;
+nitro.gif;
+smiles.gif
+  </filenames>
+</fileglob>
 <file>
 <source>loncom/interface/lontest.pm</source>
 <target dist='default'>home/httpd/lib/perl/Apache/lontest.pm</target>
@@ -3799,7 +3844,12 @@ mov_big.gif;
 move_up.gif;
 move_down.gif;
 navmap.correct.gif;
+navmap.ellipsis.gif;
 navmap.open.gif;
+navmap.page.open.gif;
+navmap.page.closed.gif;
+navmap.page.open.nomanip.gif;
+navmap.page.closed.nomanip.gif;
 navmap.wrong.gif;
 navmap.folder.open.gif;
 navmap.folder.closed.gif;
@@ -3923,6 +3973,15 @@ tested
   <status>works/verified</status>
 </file>
 <file>
+  <source>loncom/LondTransaction.pm</source>
+  <target dist='default'>home/httpd/lib/perl/LONCAPA/LondTransaction.pm</target>
+  <categoryname>system file</categoryname>
+  <description>
+	Handles a single lon-capa insternal transaction
+  </description>
+  <status>works/verified</status>
+</file>
+<file>
    <source>loncom/types/HashIterator.pm</source>
    <target dist='default'>home/httpd/lib/perl/LONCAPA/HashIterator.pm</target>
    <categoryname>system file</categoryname>
@@ -3956,10 +4015,8 @@ tested
    <categoryname>script</categoryname>
    <description>
 	  Proxy server for remote loncapa requests.
+          Needs CPAN Event module.
    </description>
-   <dependencies>
-     CPAN Event module.
-   </dependencies>
 </file>
 <file>
 <source>loncom/configuration/Configuration.pm</source>