Fix persisting which resources use feature flags

File resources get into the table a different way when they haven't been
modified by the FlaggedXmlVersioner or XmlCompatVersioner and this
addresses that path.

With this change, during compile we now find if an xml resource uses
flags and store that in the XmlResource which is then persisted to and
retrieved from the proto. This means the FlaggedXmlVersioner doesn't
have to look for them in the case that the file config or minsdk is >=
baklava.

This also moved the FeatureFlagsFilter to before we version the files.
The FeatureFlagsFilter is what strips elements behind disabled read only
flags at compile time and removed the featureFlag attribute when the
element is behind an enabled read only flag. This is so that the
FlaggedXmlVersioner doesn't have to worry if the flags it sees are
read/write or readonly. It should only ever encounter read/write flags.

Test: Automation
Bug: 377974898
Flag: android.content.res.layout_readwrite_flags
Change-Id: Ia6cbf55bc9f8d594eeb5c44c143565e93684ae2c