Well I love the idea, but I don't get how the mods should be parsed.The mod files should be separated from the others, but when you need http://www.example.com/some-file.php
to be in the index it should be moved from 'mods folder' to the index and then we go to automod use and not separating.I don't know how this to be done, then the other part should be a bit easier.
Maybe only index files should be moved to index (they may be separated in some folder like 'base') and the other styles,includes.. should not be moved and parsed from mods folder.
Then may be created or saved mod (db, cache or simple info file) information which files are moved from base and then if we want to reinstall that mod that list of base files should be read from this 'mod info file'.This can be done by mod author (like acp modules info files) or automatically via the mod parser.
Hope developers understand it, I'm not very good with English.