[sorinc03]

FullRepoManager reads relative filenames against its repository root, but FullyQualifiedNameProvider passed those filenames directly to a helper expecting root-prefixed paths. With an absolute root this raises ValueError; pyproject-based module discovery can instead resolve against the wrong working directory.

Resolve filenames against the supplied root at the provider boundary, while preserving the caller's original cache keys. Absolute filenames and the helper's outside-root checks retain their behavior. Clarify the manager's path documentation.

Fixes #1367.

Test plan

• Added real-file integration tests for relative/absolute roots and filenames, relative-import qualification, original cache keys, nested pyproject discovery, and outside-root rejection.
• Before the fix: three errors and one assertion failure in the targeted reproduction.
• 85 focused tests pass.
• Full Python 3.11 suite: 2,165 tests, 14 skips, two expected failures, no unexpected failures; 95.8% coverage.
• Repository format, lint, Pyre, and diff checks pass.

Meta CLA is already on file. Other Python/platform configurations remain for CI.