[REL-8210] account for subdirectory in ref filepaths

[blaqbern]

We were inadverntently ignoring the subdirectory option when creating File reps, which led to the tool searching zero files when using the project-level dir property in .launchdarkly/coderefs.yml (There is a workaround to just not specify the dir property, but this leads to broken links in gonfalon). The reason for this is that when using the subdirectory property, the workspace (this is the root directory that ld-find-code-refs searches under) becomes <root>/subdirectory, but the project-level dir property is relative to the repo root, so the tool would end up looking in <root>/subdirectory/subdirectory for files to scan which obviously doesn't exist. The fix here is to remove the subdirectory (if it exists) from the file's path property. Existing tests pass; added new tests for the subdirectory use-case.

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Related Jira issue: REL-8210: Code Refs - Using subdirectory flag creates broken link in LD UI when clicking View source

[sloloris]

this makes sense to me