chore(core/migration): remove legacy src/ duplicates; convert include/gitmind.h to pure umbrella; flatten CLI path to apps/cli/

[flyingrobots]

chore(core/migration): finish core migration cleanup\n\nSummary\n- Remove legacy sources under src/: edge/edge.c, edge/attributed.c, util/sha.c, util/gm_mem.h (superseded by core)\n- Convert include/gitmind.h to a pure umbrella that aggregates core public headers, no duplicate typedefs or prototypes\n- Flatten CLI path: apps/cli/cli/* → apps/cli/* (no build target change yet)\n\nRationale\n- Unblocks Sprint 1 CLI build by eliminating duplicate type definitions between the umbrella and namespaced core headers\n- Reduces confusion by removing legacy src/ code paths that are no longer built\n- Aligns tree layout with docs: apps/ contains CLI; core/ holds library and public headers\n\nTesting\n- Local Docker build/tests (Meson/Ninja) all green (14/14 unit tests)\n- No CLI build in Meson yet (separate PR will add CLI target + E2E wiring)\n\nFollow-ups\n- Add Meson CLI target now that umbrella is clean; wire E2E tests to CI\n- Tidy passes unaffected; gauntlet unchanged\n\nHousekeeping\n- build_* folders remain gitignored; safe to delete locally as they are ephemeral\n\nRequested\n- Auto-merge once checks and CodeRabbit approvals are satisfied

Summary by CodeRabbit

• Refactor

  • Public API reorganized into modular headers with an umbrella include and compile-time feature toggles.

• New Features

  • OID-first migration for edges, cache and hooks; CBOR encode/decode for attributed edges; journal commit payloads base64-encoded; per-header compile checks.

• Bug Fixes

  • Safer branch/ref handling, bounded string handling and stronger buffer/length checks in journal paths.

• Tests

  • New unit tests for CBOR/OID roundtrips, base64 handling, edge-equality semantics and journal safety.

• Chores / Removed

  • Removed legacy inline public declarations and small memory wrappers; public surface now uses OID-based types.