Add revision-checked index apply for pending file edits

[DandyLyons]

Goal

Apply explicit pending edits through the shared server mutation/codec service. Part of Phase 3 in #93; depends on #138, #90, and #82.

CLI

md-utils index apply --dry-run
md-utils index apply

This replaces the proposed update --fromSQLiteToFiles flag.

Requirements

• Define pending-edit representation and how edits enter it; keep drafts separate from disposable indexed snapshots.
• Store the baseline file revision/hash, detect external changes, and never silently overwrite conflicts.
• Encode through ResourceCodec, assess full proposed records, and apply configured policy.
• Refresh affected content, memberships, and diagnostics after persistence; refresh FTS only when enabled under Add optional body indexing with single-copy FTS5 storage #146.
• Dry-run shows concrete source changes and diagnostics without writes.
• Define per-file atomic writes and interrupted multi-file recovery; SQLite transactions do not make filesystem writes atomic as a group.
• Refresh/rebuild must not silently discard pending edits. This includes Add optional body indexing with single-copy FTS5 storage #146 indexing-mode changes, Bound collection refresh memory and reuse extraction across scopes #147 staging/recovery, and Use runtime-selected JSONB with a JSON-text compatibility mode #148 encoding-compatibility rebuilds; drafts are not disposable cache data.
• Reuse shared library mutation APIs; the CLI does not require a running HTTP server.

Acceptance criteria

• Dry-run and apply share planning/validation.
• Stale baselines produce conflicts.
• Supported edits preserve source according to the codec contract.
• Failures and interruptions report completed/pending work and recover safely.
• Overlapping resources share revisions and refreshed assessments.
• Automatic refresh does not erase pending edits.
• Indexing-mode changes and encoding rebuilds preserve pending edits and baseline revision/conflict information.

Arbitrary edits to internal document tables and automatic conflict merging are out of scope.