resourceloader: Store relative instead of absolute paths in module_deps

Make paths stored in the module_deps table relative to $IP. This ensures that when
the MediaWiki install path changes and/or if the location of the extension or skins
directory changes, that ResourceLoader's internal model is still accurate.

Previously when these paths change, ResourceLoader would exhibit various bugs.

1. Unable to detect changes in the module (if the directory no longer exists).
2. Point #1 is usually preceeded by one last cache invalidation as the content hash of the file path changes (from a valid hash to an empty string).
3. Unnecessary cache invalidation (if both old and new directories exist). This happens when a file is both an entry point (in the 'scripts' or 'styles' array) and also a file dependency. At first they are de-duplicated by array_unique. But after the disk path changes, the next check will result in the old path being fetched from module_deps, and the new path from the live configuration. This causes two changes that result in needless cache invalidation:
   • The hash list contains one more item (T111481).
   • The hash list contains both the old and new version of a file. (or even alternate versions, e.g. when a change is backported to the old wmf branch; it also affects wikis on the new branch due to the stale file path still in the database).

It seems unusual to move a MediaWiki install, and usually we recommend third
parties to run update.php if site administrators do move their wiki. However
Wikimedia's deployment system implicitly moves the MediaWiki install continously
from e.g. "/srv/mediawiki/php-1.26wmf5" to "/srv/mediawiki/php-1.26wmf6".

This caused virtually all ResourceLoader caching layers to get invalidated every
week when another wmf-branch is deployed, thus breaking these file paths, which
changes the version hash, which then invalidates the cache.

Bug: T111481
Change-Id: I173a9820b3067c4a6598a4c8d77e239797d2659c