Fix semantic indexing through symlinked source roots

[AntoineToussaint]

Closes #197.

What changed

• canonicalize a local DefaultCodeServer root through directory symlinks before cached/file/semantic operations
• preserve opaque root identity for custom VFS implementations
• advance analyzer provenance to codefly.semantic-index/v3 so prior projections cannot masquerade as results from the repaired analyzer
• prove a real symlink-rooted Python source returns COMPLETE, root-relative semantic facts

This is the generic execution-boundary fix for the failure found by Mind production session 04b-many-unit-microservices; there is no Mind-, language-, or fixture-specific handling.

Verification

• go test ./... -count=1
• go test -race ./code -count=1
• focused v3 regression rerun after the provenance change