Clone parity: depth/filter/recurse-submodules on file remotes

[Ismail-elkorchi]

Acceptance Criteria

• Clone from local path and file:// remote persists origin metadata with parity to git behavior.
• Clone accepts depth, filter, and recurseSubmodules options and writes expected repository state.
• Clone parity evidence covers behavior with git baseline validation and fsck integrity checks.

Checklist

• Implemented clone option handling in Repo.clone.
• Added node parity tests for file remote clone with depth/filter/recurse-submodules.
• Updated invariants and parity matrix evidence text.
• Updated check scripts to gate parity coverage for the new clone signals.
• Ran node scripts/check --runtime=node successfully.

Simulated Role Reviews

Product review

Findings:

• Clone options previously rejected in API are now executed for supported local and file remotes.
  Changes made:
• Added clone source resolution, origin config hydration, shallow boundary writing, and recursive submodule clone flow.
  Evidence pointers:
• src/index.ts
• tests/node/clone-receive-pack.test.mjs

QA review

Findings:

• Parity coverage needed explicit checks for option flags and file remote path handling.
  Changes made:
• Added clone file remote supports depth filter and recurse-submodules parity INV-FEAT-0053 test and retained baseline git comparison.
  Evidence pointers:
• tests/node/clone-receive-pack.test.mjs
• scripts/check

Security review

Findings:

• Clone URL parsing must reject unsupported schemes and maintain path safety while materializing trees and submodules.
  Changes made:
• Added source-resolution guards for scheme handling and kept worktree path validation in clone materialization and submodule flow.
  Evidence pointers:
• src/index.ts
• node scripts/check --runtime=node

Performance review

Findings:

• Option support should preserve deterministic behavior and avoid repeated network assumptions for local/file cloning.
  Changes made:
• Implemented direct object/ref reuse from source gitdir and deterministic traversal for shallow boundary computation.
  Evidence pointers:
• src/index.ts
• tests/node/clone-receive-pack.test.mjs

Maintainer review

Findings:

• Governance artifacts must stay aligned with implemented parity scope and invariant wording.
  Changes made:
• Updated API docs, parity matrix text, invariant statement, and parity gate checks for depth/filter/recurse-submodules and file remote support.
  Evidence pointers:
• docs/api.md
• docs/parity-matrix.md
• spec/invariants.yaml
• scripts/parity_matrix_check