Make sure file paths are valid before calling initAfterRead

[magnesj]

Currently initAfterRead is called as part of PdmDocument::readFile(). At this point, the file path modification operations in RiaApplication is not executed yet. Several operations related to a valid file path would be useful in initAfterRead.

Suggested changes

• avoid calling framework functions in PdmDocument::readFile
• in RiaApplication, call resolveReferencesRecursively and initAfterReadRecursively after file path operations are completed
• move updatedFilePathFromPathId to private section in RimProject