I'm using AUCTeX 11.87 along with emacs 24.3 for writing my LaTeX documents. This is working nicely with one exception: The parsing.
My document structure is as follows:
./ Master.tex Chapter_1.tex Chapter_2.tex ... header/ header/header.tex header/packages.tex header/options.tex ...
Where Master.tex \inputs header.tex which in turn inputs all files in header/. Furthermore Master.tex includes the Chapter_N.tex files within the document environment.
Here comes the problem: AUCTeX does not generate the parse files (the ones in the auto folder) until I have actually opened the file. Meaning that until I have not opened and saved the header/packages.tex and header/header.tex files AUCTeX does not know about the loaded packages and thus their commands/environments.
An now the question: Can I force AUCTeX to (re)parse the whole source-tree (and then reload the style hooks for all open documents)?
If all files are in the same directory, or in subdirectories under it, open the master file and issue M-x TeX-auto-generate RET and as TeX file or directory insert the directory of the master file and as AUTO lisp directory the auto/ subdirectory of the previous directory.
For instance, if your master file is placed in ~/my-document/, insert ~/my-document/ at the first prompt and ~/my-document/auto at the second one (you can also use relative paths if you prefer them).