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Used usage.pl to find out which help files do not exist in the manual and added them.

<texxml>
	<title name="LON-CAPA Course Administrator's Manual" />
	<file name="Course_Manual_Title_Page.tex" />

	<section name="System Overview">
		<file name="What_Is_LON-CAPA.tex" />
		</section>

	<section name="Help">
		<subsection name="Where to find additional help">
			<file name="Additional_Help.tex" />
			</subsection>
		<subsection name="Requesting New Features and Submitting Suggestions">
			<file name="Bugzilla.tex" />
			</subsection>
		</section>

	<section name="Logging In">
		<subsection name="Roles Screen">
			<file name="Roles_Screen.tex" />
			</subsection>
		<subsection name="Remote Control and Menu Mode">
			<file name="Remote_Menu.tex" />
			</subsection>
		</section>


	<section name="Setting Preferences">
		<subsection name="Change Password">
			<file name="Change_Password.tex" />
			</subsection>
		<subsection name="Nickname and Anonymous Discussion Screen Name">
			<file name="Prefs_Screen_Name_Nickname.tex" />
			</subsection>
		<subsection name="Message forwarding and notification address">
			<file name="Prefs_Forwarding.tex" />
			</subsection>
		<subsection name="The 'About Me' Personal Information Screen">
			<file name="Prefs_About_Me.tex" />
			</subsection>
		<subsection name="Color Scheme">
			<file name="Change_Colors.tex" />
			</subsection>
		<subsection name="Language Preferences">
			<file name="Prefs_Language.tex" />
			</subsection>
		</section>

	<section name="Exploring Your Course">
		<file name="Exploring_Your_Course.tex" />
		<subsection name="Course Initialization Helper">
			<file name="Helper_Course_Initialization.tex" />
			</subsection>
		<subsection name="Help">
			<file name="Help.tex" />
			</subsection>
		<subsection name="Navigation Screen">
			<file name="Navigation_Screen.tex" />
			</subsection>
                <subsection name="Edit Syllabus">
			<file name="Edit_Syllabus.tex" />
			</subsection>
		</section>


	<section name="DOCS - Course Documents">
		<file name="Docs_Overview.tex" />
		<subsection name="Main Course Documents">
			<file name="Docs_Main_Course_Documents.tex" />
			</subsection>
		<subsection name="Adding Material to Your Course">
			<file name="Docs_Adding_Course_Doc.tex" />
			</subsection>
		<subsection name="Special Documents: Folders">
			<file name="Docs_Adding_Folders.tex" />
			</subsection>
		<subsection name="Imported Documents: Import">
			<file name="Docs_Importing_LON-CAPA_Resource.tex" />
			</subsection>
		<subsection name="Imported Documents: Search">
			<file name="Docs_Search.tex" />
			</subsection>
		<subsection name="Imported Documents: Load Map">
			<file name="Docs_Load_Map.tex" />
			</subsection>
		<subsection name="Special Documents: Templates">
			<file name="Docs_Creating_From_Template.tex" />
			<subsubsection name="Special Documents: Syllabus">
                        	<file name="Docs_About_Syllabus.tex" />
				<file name="Docs_Adding_Syllabus.tex" />
				<file name="Syllabus_ExtLink.tex" />
                        	</subsubsection>
			<subsubsection name="Special Documents: Simple Page">
				<file name="Docs_About_Simple_Page.tex" />
				</subsubsection>
			<subsubsection name="Special Documents: Bulletin Board">
				<file name="Docs_About_Bulletin_Board.tex" />
				</subsubsection>
			<subsubsection name="Special Documents: My Personal Info">
				<file name="Docs_About_My_Personal_Info.tex" />
				</subsubsection>
			<subsubsection name="Editing Templated Special Documents">
				<file name="Docs_Editing_Templated_Pages.tex" />
				</subsubsection>
			<subsubsection name="Alternatives">
				<file name="Docs_Alternatives.tex" />
				</subsubsection>
			</subsection>
		<subsection name="Special Documents: Composite Page">
			<file name="Docs_Adding_Pages.tex" />
			</subsection>
		<subsection name="Special Documents: External Resource">
			<file name="Docs_Adding_External_Resource.tex" />
			</subsection>
		<subsection name="Special Documents: Navigate Content">
			<file name="Docs_Navigate_Content.tex" />
			</subsection>
		<subsection name="Special Documents: Score Upload Form">
			<file name="Docs_Score_Upload_Form.tex" />
			</subsection>
		<subsection name="Special Documents: Simple Problem">
			<file name="Docs_Simple_Problem.tex" />
			<subsubsection name="1 out of N Multiple Choice">
				<file name="Docs_Radio.tex" />
				</subsubsection>
                        <subsubsection name="Option Response">
                                <file name="Docs_Option_Response.tex" />
                                </subsubsection>
                        <subsubsection name="Essay">
                                <file name="Docs_Essay.tex" />
                                </subsubsection>
                        <subsubsection name="Short String Response">
                                <file name="Docs_String_Response.tex" />
                                </subsubsection>
			</subsection>
		<subsection name="Uploading a New Main Course Document">
			<file name="Docs_Uploading_From_Harddrive.tex" />
			</subsection>
                <subsection name="Verify Content">
                        <file name="Docs_Verify_Content.tex" />
                        </subsection>
                <subsection name="Check/Set Resource Versions">
                        <file name="Docs_Check_Resource_Versions.tex" />
                        </subsection>
                <subsection name="Dump Course Docs to Construction Space">
                        <file name="Docs_Dump_Course_Docs.tex" />
                        </subsection>
                <subsection name="Supplemental DOCS">
                        <file name="Docs_Supplemental.tex" />
                        </subsection>
		</section>

	<section name="Managing the Class List">
		<subsection name="Class List Management">
			<file name="Course_Create_Class_List.tex" />
			<subsubsection name="Add a Student">
				<file name="Course_Add_Student.tex" />
				</subsubsection>
			<subsubsection name="Drop a Student">
				<file name="Course_Drop_Student.tex" />
				</subsubsection>
			</subsection>
		<subsection name="Converting to CSV">
			<file name="Course_Convert_To_CSV.tex" />
			</subsection>
		<subsection name="Course Chart to Excel">
			<file name="Course_Chart_To_Excel.tex" />
			</subsection>
		<subsection name="Modifying Student Data">
			<file name="Course_Modify_Student_Data.tex" />
			</subsection>
		<subsection name="Viewing the Class List">
			<file name="Course_View_Class_List.tex" />
			</subsection>
		</section>

	<section name="Course Parameters">
		<file name="Course_Setting_Parameters.tex" />
		<subsection name="Feedback Adresses">
			<file name="Course_Feedback_Addresses.tex" />
			</subsection>
		<subsection name="Top-level Sequence">
			<file name="Course_Toplevel_Seq.tex" />
			</subsection>
		<subsection name="Problem Weight">
			<file name="Course_Problem_Weight.tex" />
			</subsection>
		<subsection name="Setting Parameters for an Individual Student">
			<file name="Course_User_Parameter.tex"
			</subsection>
		</section>

	<section name="Problem Parameters">
		<subsection name="Overview">
			<file name="Problem_Parameters.tex" />
			</subsection>
		<subsection name="Allowing Collaboration on an Essay Problem">
			<file name="Course_Maximum_Collaborators.tex" />
			</subsection>
		</section>


	<section name="Course Communication System">
		<file name="Course_Message_Access.tex" />
		<subsection name="Send Communication Messages to User(s)">
			<file name="Sending_Email.tex" />
			</subsection>
		<subsection name="Broadcast Message to Course">
			<file name="Course_Broadcast_Message.tex" />
			</subsection>
		<subsection name="Critical Messages">
			<file name="Course_Critical_Message.tex" />
			</subsection>
		<subsection name="Disabling Discussion">
			<file name="Course_Disable_Discussion.tex" />
			</subsection>
		<subsection name="Recording Notes and Face-To-Face Communication">
			<file name="Course_Face_To_Face_Records.tex" />
			</subsection>
		</section>

	<section name="Discussion Posts and Feedback">
		<subsection name="Resource Discussion">
			<file name="Resource_Discussion.tex" />
			</subsection>
		<subsection name="Giving Feedback">
			<file name="Leaving_Feedback.tex" />
			</subsection>
		<subsection name="Change the way Discussion Posts are Displayed">
			<file name="Change_Discussion_Display.tex" />
			</subsection>
		</section>


	<section name="Chart Student Progress">
		<file name="Chart_Description.tex" />
		<subsection name="Homework Performance Overview">
			<file name="Course_Homework_Performance_Overview.tex" />
			</subsection>
		<subsection name="Data Output Selection">
			<file name="Chart_Output_Data.tex" />
			</subsection>
		<subsection name="Output Formats">
			<file name="Chart_Output_Formats.tex" />
			</subsection>
		</section>


	<section name="Grades and Submissions">
		<tex content="By default, LON-CAPA computer grades all resources except for essay questions and score upload forms.  Sometimes, an instructor will need to hand-grade a problem though" />
		<file name="Course_Manually_Grade_Problem.tex" />
		<subsection name="Student Grade Override">
			<file name="Course_Student_Grade_Override.tex" />
			</subsection>
		<subsection name="Viewing Student Problems">
			<file name="Course_Student_Work.tex" />
			</subsection>
		</section>

	<section name="Statistics">
		<subsection name="Problem Analysis">
			<file name="Analysis_Analyze_Over.tex" />
			</subsection>
		<subsection name="Overall Problem Statistics">
			<file name="Statistics_Sequence.tex" />
			<file name="Statistics_Overall_Key.tex" />
			</subsection>
		<subsection name="Clear and Update Cache">
			<file name="Statistics_Cache.tex" />
			</subsection>
		</section>


	<section name="Spreadsheet">
		<subsection name="Introduction to the Spreadsheet">
			<file name="Spreadsheet_About.tex" />
                	<file name="Spreadsheet_Student_View.tex" />
			</subsection>
		<subsection name="Spreadsheet Organization">
			<file name="Spreadsheet_Hierarchy.tex" />
			<file name="Spreadsheet_Layout.tex" />
			<file name="Spreadsheet_Levels.tex" />
                       	<file name="Spreadsheet_Export_Row.tex" />
                       	<file name="Spreadsheet_Template_Row.tex" />
			</subsection>
		<subsection name="Modifying the Spreadsheet">
                	<file name="Spreadsheet_Files.tex" />
                	<file name="Spreadsheet_Editing.tex" />
                	<file name="Spreadsheet_Cell_Editing.tex" />
                	<file name="Spreadsheet_Functions.tex" />
                	<file name="Spreadsheet_Referencing_Cells.tex" />
                	<file name="Spreadsheet_Referencing_Parameters.tex" />
			<file name="Spreadsheet_Parms.tex" />
                	<file name="Spreadsheet_HowTo.tex" />
                	<file name="Spreadsheet_HowTo_Assessments.tex" />
			</subsection>
		</section>


	<section name="Student Grade Access">
		<subsection name="Changing Course Parameters for Student Access of Spreadsheet Data">
			<file name="GradingOptions.tex" />
			</subsection>
                </section>


	<section name="LON-CAPA Exams">
		<file="exam_basics.tex" />
		</section>

	<section name="Misc.">
		<subsection name="Prepare a Printable PDF Document">
			<file name="Print_Resource.tex" />
			</subsection>
		<subsection name="Adding Instructors and Teaching Assitants to Your Course">
			<file name="Course_Add_Other.tex" />
			<subsubsection name="Change Privileges of a User">
				<file name="Course_Change_Privileges.tex" />
				</subsubsection>
			<subsubsection name="Creating a Custom Role">
				<file name="Course_Editing_Custom_Roles.tex" />
				</subsubsection>
			</subsection>
		<subsection name="Course Calendar">
			<file name="Calendar_Add_Announcement.tex" />
			<file name="Calendar_Remove_Announcement.tex" />
			</subsection>
		<subsection name="Course Chat">
			<file name="Course_Chat.tex" />
			</subsection>
		<subsection name="Evaluating a Resource">
			<file name="Course_User_Evaluation.tex" />
			</subsection>
		<subsection name="Searching the LON-CAPA Resource Pool">
			<file name="Searching.tex" />
			<file name="Search_Basic.tex" />
			<file name="Search_Advanced.tex" />
			</subsection>
		<subsection name="Bookmarks">
			<file name="Bookmarks.tex" />
			</subsection>
		<subsection name="Annotations">
			<file name="Annotation.tex" />
			</subsection>
		<subsection name="On Deleting Courses">
			<file name="Course_Deleting.tex" />
			</subsection>
		</section>

	</texxml>