fix(graph): re-absolutize repo-scoped bundle paths on import (#1509) - #1627

Summary

Fixes #1509 (GSSoC'26).

Repo-scoped export (cgc bundle export --repo) correctly rewrites absolute paths to portable . / ./… form. Import never inverted that rewrite, so every imported bundle landed with Repository.path = ".". _check_existing_repository then matched on that path, so loading a second registry bundle (for example flask, then requests) was always refused as a duplicate. --clear was the only workaround and it wiped the first bundle, which breaks the bundle-registry use case (#1180).

Even if the existence check were skipped, File MERGE keys such as ./README.md and Function/Class uids built from name + path + line_number would collide across repos.

Export is unchanged. Relative .cgc contents stay portable. Import is now the inverse of the rewrite.

Problem

1. False duplicate: after import, metadata.repo_path and the Repository node path are ".". The path MATCH in _check_existing_repository then hits any previously imported repo-scoped bundle.
2. File primary-key collision: _PK_MAP MERGEs File/Directory/Repository on path, so ./README.md from two repos would become one node.
3. Function/Class identity: _UID_PARTS builds uid from name + path + line_number. Relative paths would make parse at line 1 collide across repos.

Solution

On import, rebase . / ./… onto a per-bundle destination root:

~/.codegraphcontext/bundles/<sanitized_repo>

Example: pallets/flask becomes slug pallets__flask. Tests can pass destination_root= so they never touch the real home directory.

Behaviour:

• Rebase metadata.repo_path and all bundle-relative node/edge string properties before MERGE.
• _check_existing_repository still matches by name (same repo twice is still a duplicate) but does not treat . / ./… as an identifying path.
• After rebase, Function/Class uid is rebuilt from _UID_PARTS so identity includes the dest root.
• _delete_repository refuses to delete when r.path is ., because STARTS WITH "./" would wipe every repo-scoped import.

Upstream encryption/signing (password, verify_key, payload_path) is preserved after rebase onto main.

Files changed

• src/codegraphcontext/core/cgc_bundle.py — path helpers, import rebase, existence-check hardening, delete guard. Also threads destination_root on import_from_bundle without breaking password / verify_key.
• tests/unit/core/test_bundle_repo_scoped_import.py — new unit tests (mocked driver, no live graph DB).

CLI and MCP call sites are unchanged. They pick up the default dest root.

Tests performed

Command:

python -m pytest tests/unit/core/test_bundle_repo_scoped_import.py tests/unit/core/test_bundle_edge_zero_id.py tests/unit/core/test_bundle_identifier_validation.py tests/unit/core/test_bundle_pk_map_coverage.py -q

Result: 87 passed.

Covered:

• Rebase of ., ./README.md, .\src\a.py; absolute paths and os.path left alone.
• Slug pallets/flask -> pallets__flask; empty -> unknown.
• Path "." does not issue MATCH (r:Repository {path: $path}); real absolute paths still do; name match still runs.
• Two File rows both ./README.md MERGE with distinct pk_val values (flask vs requests dest roots).
• Function uid contains dest root, not ./.
• _delete_repository no-ops when found path is ".".

Related existing bundle tests still pass: edge zero-id, identifier validation, _PK_MAP coverage.

Checklist

• Focused on a single bug (bug(graph): repo-scoped bundles export their root path as ., so importing a second bundle is always refused as a duplicate #1509)
• Tests added for the fix
• Linked to the issue
• Rebased onto upstream/main