There are many files used to produce the several output formats, and to store the many text and information needed to generate the files. These are the most important ones, you should know about:
The main file for the documentation. It is supposed to be only a "glue" between the other parts, containing only part titles and entity references to chapters. It is generated from manual.xml.in when you run configure.
Contains entity definitions for all files. Entities for the XML files are generated by configure, so you should not edit this file.
Global internal text entities for all the XML files. This is where all the external links, email addresses, and "macros" are stored.
DSSSL style sheets we use to generate the available formats of the manual.
XSL style sheets to generate HTML, phpweb, HTMLHelp and print output from the manual XML sources.
Contains local entities used by this language. Some common ones are the main part titles, but you should also put entities used only by this language's files here.
Longer often used XML snippets translated to this language. Including common warnings, notes, etc.
This file is used to store all central translation info, like a small intro text for translators, the persons list, and the files under translation / modification. This file is not present in the English tree.
The PHP Manual XML source is organized into directories. The biggest part is the extension reference, which is stored in the reference directory of your language.