The files do this:

Makefile               -- so you can run make :)
after.js               -- shortened from originalafter.js
before.js              -- just includes a variable name, don't edit
compkey.txt            -- decompression key, generated by unusedcompress.php
compressed.txt         -- double compressed function list, generated by 
                          unusedcompress.php
funclist.txt           -- includes the list of all functions, genereted by 
                          makefunclist.php from manual_en_contents.txt
functions.js           -- the final file, include before </body>
index.html             -- just for testing
makefunclist.php       -- processes manual_en_contents.txt and extracts 
                          the names of all functions (better than funclist.txt
                          from cvs/phpdoc/funclist.txt, which is out of date)
manual_en_contents.txt -- list of files in phpweb/manual/en/ directory; this 
                          is the file to update when new functions appear
middle.js              -- similar to before.js
originalafter.js       -- most of javascript; edit for fixes and whatnot
prefixcompress.php     -- does multi-level prefix compression; 
prefixcompressed.txt   -- prefix compressed version of funclist.txt
processafter.php       -- processes originalafter.js and shortens it by 
                          removing comments, spaces, newlines and shortening
                          variable and function names; may require editing if 
                          you update originalafter.js as it contains a list of
                          unchangeable tokens (e.g. while, getElementById)
unusedcompress.php     -- does compression by replacing sequences of
                          characters by unused characters


So, if new functions become available, update manual_en_contents.txt and 
run make.

If you want to edit the javascript code, update originalafter.js and run
make.