Fix symlinked source discovery

[longlho]

Summary:

• Follow symlinked source directories during project discovery.
• Preserve logical entry paths instead of canonicalizing them out of the analysis root.
• Add a runfiles-style regression test with symlinked config and app sources.

Verification:

• bazel test //crates/codescythe:codescythe_test
• bazel test //...
• Manual CLI fixture: real tree and symlinked runfiles tree both report app/dead.ts