Persist parser source snapshots and reject changed-during-parse results

[TheGreenCedar]

Parent: #911

Problem

Parser-backed indexing reads source bytes before parsing but records filesystem
metadata later. A concurrent edit can therefore publish graph data from old
bytes while stamping it with the newer modification time, allowing refresh
planning to treat stale graph data as current.

Scope

Persist the identity of the bytes actually parsed and reject results when the
source changes before publication. Keep this slice inside indexer/store source
snapshot integrity; do not alter repository identity, discovery/deletion
semantics, or runtime publication ownership.

Acceptance Criteria

• Add a nullable stored content hash for parser-backed file projections,
  with an additive schema migration that preserves legacy rows.
• Hash the source bytes already read for parsing; do not add a redundant
  pre-parse read.
• Re-read and compare the source before accepting parser or artifact-cache
  results.
• Stamp the captured metadata only when the verified bytes still match.
• Convert changed-during-parse/cache results into an incomplete file-level
  retry error and do not publish graph data from the stale bytes.
• Carry hashes through the existing projection batch/storage boundary
  without adding content identity to the widely constructed FileInfo.
• Clear stored hashes for refreshed rows that do not provide a verified
  content identity.
• Expose one focused store read for proof and later Replace mtime-only freshness with content and completeness identity #911 planning work.
• Cover unchanged parsing, artifact-cache hits, changed-during-parse with a
  restored same timestamp, projection round-trip/clearing, and migration
  from the prior schema.
• Update the changelog and nearest testing/architecture documentation.

Non-Goals

• Same-timestamp refresh planning for unchanged files
• Lossless filesystem discovery and deletion gating
• Non-parser collector snapshots
• Repository identity or path equality (Migrate repository identity and path equality for case-sensitive repos #913/Version the lossless repository identity contract #974)
• Runtime staged-publication/crash behavior (Complete the atomic publication crash and cancellation matrix #955/test publication fault matrix #973)

Verification

• Focused codestory-store migration/projection tests
• Focused codestory-indexer source-snapshot and cache tests
• cargo fmt --all -- --check
• Relevant package clippy checks with warnings denied
• git diff --check

Run Cargo commands serially.

Refs #899