Start fixing missing documentation

doc/Command_Index_User.tex

@@ -1784,6 +1784,10 @@ \subsection{Distances}\label{distances}
 The space between the lines and the bottom of the text.
 \end{gdimension}
 
+\begin{gdimension}{noteadditionalspacelinestext}
+The per-note additional space between lines and the bottom of the text.
+\end{gdimension}
+
 \begin{gdimension}{spacebeneathtext}
 The space beneath the text.
 \end{gdimension}

doc/Command_Index_internal.tex

@@ -1435,6 +1435,9 @@ \section{Gregorio\TeX{} Controls}
   \#2 & any & the second argument\\
 \end{argtable}
 
+\macroname{\textbackslash gre@parshape@dims}{}{gregoriotex-main.tex}
+Holds the \verb=\parshape= information needed to shape the score around the initial.
+
 \subsection{Auxiliary File}
 Gregorio\TeX\ creates its own auxiliary file (extension \texttt{gaux}) which it uses to store information between successive typesetting runs.  This allows for such features as the dynamic interline spacing.  The following functions are used to interact with that auxiliary file.
 
@@ -1963,7 +1966,7 @@ \subsection{Flags}
 Boolean indicating whether the above lines text should be shown.
 
 \macroname{\textbackslash gre@count@initiallines}{}{gregoriotex-syllable.tex}
-Number of lines the initial takes up.  Currently limited to 0, 1, or 2.  Not currently a count, but will be changed to one in 5.0.
+Number of lines the initial takes up.
 
 \macroname{\textbackslash ifgre@rewritethissyllable}{}{gregoriotex-syllable.tex}
 Boolean indicating that a syllable should be rewritten to improve ligature rendering.
@@ -1977,6 +1980,15 @@ \subsection{Flags}
 \macroname{\textbackslash ifgre@noteadditionalspacelinestext}{}{gregoriotex-main.tex}
 Boolean indicating that the additional space needed between the notes and the lyrics due to really low notes should follow the user setting of noteadditionalspacelinestext (as opposed to being calculated automatically, the default).
 
+\macroname{\textbackslash ifgre@alteration@effect@note}{}{gregoriotex-signs.tex}
+Boolean indicating that soft alterations should last until they apply to a single note (i.e. all soft alterations will be printed).
+
+\macroname{\textbackslash ifgre@alteration@effect@line}{}{gregoriotex-signs.tex}
+Boolean indicating that soft alterations should last until the end of line.
+
+\macroname{\textbackslash gre@count@parsecomma@cur}{}{gregoriotex-common.tex}
+When parsing a comma separated list of options, the comma we are currently processing.
+
 
 \subsection{Boxes}