Documentation mostly works now!

Replaced f90pdf call in make_protex_file with a protex script from the internet
and then call pdflatex several times on resulting tex file. The table of
contents isn't quite complete, but scanning through the rest of the document it
looks okay.

doc/.gitignore

@@ -0,0 +1 @@
+protex_out/*

doc/make_protex_file

@@ -1,9 +1,12 @@
-#!/bin/bash
+#!/bin/bash -e
 
 SRC=../src
 DRIVE=$SRC/drivers
 SHARE=$SRC/shared
-f90pdf                                       \
+
+mkdir -p protex_out
+rm -f protex_out/protex_documentation.*
+./protex                                     \
        $SHARE/cvmix_kinds_and_types.F90      \
        $SHARE/cvmix_background.F90           \
        $SHARE/cvmix_shear.F90                \
@@ -20,7 +23,12 @@ f90pdf                                       \
        $DRIVE/cvmix_tidal_Simmons.F90        \
        $DRIVE/cvmix_ddiff_drv.F90            \
        $DRIVE/cvmix_kpp_drv.F90              \
-       $SRC/cvmix_io.F90
+       $SRC/cvmix_io.F90 >                   \
+       protex_out/protex_documentation.tex
 
-rm -f output.tex
-mv -f output.pdf protex_documentation.pdf
+cd protex_out
+pdflatex protex_documentation.tex
+pdflatex protex_documentation.tex
+pdflatex protex_documentation.tex
+pdflatex protex_documentation.tex
+cp -f protex_documentation.pdf ../