rego+bundle: Fix issues underlying #3209 (#3444)

* bundle: cleanup path before setting it as baseDir

GetBundleDirectoryLoader will do it again, but we need the cleaned-up
`path` to avoid "file:/" parts erroneously making it into the bundle's
ModuleFile structs. GetBundleDirectoryLoader is shared with the server,
so we'll keep that as-is.

* rego: avoid (*Bundle).ParsedModules(..)

Using this will prefix a path that is already complete. Using ModuleFile's
Path instead, we get the already-resolved path.

Signed-off-by: Stephan Renatus <stephan.renatus@gmail.com>