logs: migrate to molecular CoT JSON protocol, fix regressions

- Replace BeliefFormatter with CotJsonFormatter (single-line JSON with
  ts, level, trace_id, src, marker, intent, payload, error, span_id)
- Migrate belief_scope to use cot_log() for structured JSON output
- Update monkey-patched reason/reflect/explore to pass extra= dict
- Strip 200+ inline [REASON]/[REFLECT]/[EXPLORE] markers from 50+ files
- Remove belief_scope from hot-path utilities (_parse_datetime,
  _json_load_if_needed) to eliminate startup log noise
- Register TraceContextMiddleware in app.py (was implemented but unused)
- Seed trace_id in startup_event/shutdown_event for background tasks
- Fix broken relative imports in translate routes (3 dots → 4 dots)
- Migrate 43 translate_routes log calls to logger.reason/explore
- Fix SyntaxError (positional arg after extra=) in _repo_operations_routes
- Fix IndentationError in rbac_permission_catalog except-block
- Add smoke test tests/test_smoke_app.py (catches import errors before run)

.opencode/command/speckit.semantics.md

@@ -19,11 +19,12 @@ Ensure the repository adheres to the active GRACE semantic protocol using AXIOM
 1. **ROLE: Orchestrator** — coordinate semantic maintenance at the workflow level.
 2. **MCP-FIRST** — use AXIOM task-shaped tools for discovery, context, audit, impact analysis, and safe mutation planning.
 3. **STRICT ADHERENCE** — follow the local semantic authorities:
-   - `.opencode/skills/semantics-core/SKILL.md`
-   - `.opencode/skills/semantics-contracts/SKILL.md`
-   - `.opencode/skills/semantics-python/SKILL.md`
-   - `.opencode/skills/semantics-svelte/SKILL.md`
-   - `.opencode/skills/semantics-testing/SKILL.md`
+      MANDATORY USE `skill({name="semantics-core"})`, 
+      `skill({name="semantics-contracts"})`, 
+      `skill({name="semantics-belief"})`, 
+      `skill({name="semantics-python"})`, 
+      `skill({name="semantics-svelte"})`, 
+      `skill({name="molecular-cot-logging"})`
    - relevant `docs/adr/*`
 4. **NON-DESTRUCTIVE** — do not remove business logic; only add or correct semantic markup unless the user requested implementation changes.
 5. **NO PSEUDO-CONTRACTS** — do not mechanically inject fake semantic boilerplate.