fix(storage): recover topology batches before generation commit

[DecisionNerd]

Closes #935

Summary

• persist authenticated preparing/durable rewrite intents and publish generation authority last
• recover descriptor-relatively with retained root, parent, temporary, prior destination, and installed-file identities
• fail closed on substitution, truncation, traversal, stale authority, cross-root state, and ambiguous replay
• make concurrent lock bootstrap create-exclusive and document the recovery state machine and bounds

Validation

• cargo test -p graphforge-storage --no-fail-fast (654 passed, 2 ignored; integration suites green)
• cargo test -p graphforge-filesystem (13 passed)
• cargo clippy -p graphforge-filesystem -p graphforge-storage --lib -- -D warnings
• bazelisk test //crates/graphforge-filesystem:graphforge_filesystem_test //crates/graphforge-storage:graphforge_storage_test
• make pre-push-fast
• make docs-build (107 pages; extension-doc contract passed)
• cargo fmt --all -- --check
• git diff --check

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Summary by CodeRabbit

• New Features

  • Added durable recovery for interrupted graph-file rewrites, including validation against tampering, stale data, and path substitutions.
  • Added support for tracking auxiliary rewrite receipts and topology/search generation updates.

• Bug Fixes

  • Improved concurrent file creation so all callers consistently use the same file.
  • Restricted operational-file filtering to recognized artifacts, preventing similarly named files from being overlooked.
  • Improved cleanup and recovery after interrupted transactions.

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Walkthrough

Changes

The change adds authenticated, crash-safe recovery for topology-aware graph rewrites. It updates generation commits, staged-file cleanup, writer integration, operational-file filtering, lock conformance checks, and concurrent child-file creation tests.

Durable rewrite recovery

Layer / File(s)	Summary
Stable exclusive child-file creation crates/graphforge-filesystem/src/lib.rs	Unix and Windows implementations now use exclusive creation followed by reopen-existing handling. A concurrent test verifies one stable file identity.
Authenticated rewrite journal contract crates/graphforge-storage/src/durable_rewrite.rs	The journal records authenticated paths, file identities, digests, generations, auxiliary receipts, and bounded durable intent state.
Commit and recovery integration crates/graphforge-storage/src/durable_rewrite.rs, crates/graphforge-storage/src/generation.rs, crates/graphforge-storage/src/staging.rs, crates/graphforge-storage/src/writer.rs, crates/graphforge-storage/src/lib.rs	Topology-aware commits recover prior intents, install staged data before generation authority, expose auxiliary receipt support, and clean up through idempotent recovery. Tests cover validation failures, substitutions, ordinary recovery, and crash phases.
Operational-file classification and lock validation crates/graphforge-storage/src/graph_files.rs, crates/graphforge-storage/src/project_generation.rs, crates/graphforge-api/tests/knowledge_isolation.rs, scripts/ci/*	Traversal and validation ignore only canonical operational files. CI checks accept the rewrite lock and reject unexpected names and symlinks.

Estimated code review effort: 5 (Critical) | ~120 minutes

Merge Risk: 🟡 Moderate · up to 91241

Generation reads now perform recovery even when no rewrite is pending, which can make missing or read-only roots fail instead of returning the expected empty state and adds unnecessary exclusive-lock and synchronization work. Merge readiness requires limiting recovery to cases with a rewrite marker, or explicitly accepting this behavior.

Sequence Diagram(s)

sequenceDiagram
  participant Writer
  participant Generation
  participant DurableRewrite
  participant Filesystem
  Writer->>Generation: submit topology-aware rewrite
  Generation->>DurableRewrite: commit staged data and generation pair
  DurableRewrite->>Filesystem: publish authenticated intent
  DurableRewrite->>Filesystem: install staged destinations
  DurableRewrite->>Filesystem: publish generation authority last
  DurableRewrite-->>Generation: return committed generation pair
  Generation-->>Writer: return commit result

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🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 46.51% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 86 functions across 13 files.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly identifies the primary change: recovering topology-aware rewrite batches before generation commit.
Description check	✅ Passed	The description clearly states the purpose, linked issue, implementation scope, and validation commands. It does not reproduce all template headings or checklist selections, but the core required info…
Linked Issues check	✅ Passed	The reviewable changes address issue #935. They add authenticated durable intents, identity-safe descriptor-relative recovery, staged-file preservation, generation-last publication, auxiliary receipt …
Out of Scope Changes check	✅ Passed	The changes remain focused on durable topology rewrite recovery and its supporting lock-file classification, filesystem identity behavior, participant validation, and CI coverage. No unrelated code ch…

Full details: Description check

Explanation

The description clearly states the purpose, linked issue, implementation scope, and validation commands. It does not reproduce all template headings or checklist selections, but the core required information is present.

Full details: Linked Issues check

Explanation

The reviewable changes address issue #935. They add authenticated durable intents, identity-safe descriptor-relative recovery, staged-file preservation, generation-last publication, auxiliary receipt binding, fail-closed validation, idempotent recovery, failure-barrier tests, and exclusive lock bootstrap. Existing storage and filesystem tests are reported as passing.

Full details: Out of Scope Changes check

Explanation

The changes remain focused on durable topology rewrite recovery and its supporting lock-file classification, filesystem identity behavior, participant validation, and CI coverage. No unrelated code changes are evident.

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Actionable comments posted: 1

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Inline comments:
In `@crates/graphforge-storage/src/generation.rs`:
- Around line 128-131: Update read_generation_state to probe for
.graphforge-rewrite-v1.json before invoking durable_rewrite::recover; recover
only when that marker exists, then call read_generation_state_raw. Preserve
generation-0 behavior for missing roots and avoid recovery side effects and
exclusive locking for clean or read-only roots.

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📥 Commits

Reviewing files that changed from the base of the PR and between 5c7260d and 9124179.

⛔ Files ignored due to path filters (3)

• docs/adr/0013-project-generation-protocol.md is excluded by !**/*.md, !**/docs/**
• docs/book/architecture/concurrency-recovery.md is excluded by !**/*.md, !**/docs/**
• docs/book/architecture/storage.md is excluded by !**/*.md, !**/docs/**

📒 Files selected for processing (13)

• crates/graphforge-api/tests/knowledge_isolation.rs
• crates/graphforge-filesystem/src/lib.rs
• crates/graphforge-storage/src/durable_rewrite.rs
• crates/graphforge-storage/src/generation.rs
• crates/graphforge-storage/src/graph_files.rs
• crates/graphforge-storage/src/lib.rs
• crates/graphforge-storage/src/project_generation.rs
• crates/graphforge-storage/src/staging.rs
• crates/graphforge-storage/src/writer.rs
• scripts/ci/bulk-construction-conformance.py
• scripts/ci/concurrency-short-gate.py
• scripts/ci/test-bulk-construction-conformance.py
• scripts/ci/test-concurrency-short-gate.py

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