chore: add filtered selection file for MCP-unique tasks 121-141

Subset of selected_mcp_unique_tasks.json containing only the 21 new
tasks (use case IDs 121-141) for targeted staging runs.

Also regenerates stale script registry and agent navigation.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: sjarmak

.github/workflows/docs-consistency.yml

@@ -20,3 +20,6 @@ jobs:
 
       - name: Validate docs references
         run: python3 scripts/docs_consistency_check.py
+
+      - name: Verify generated agent navigation artifacts are fresh
+        run: python3 scripts/refresh_agent_navigation.py --check

.github/workflows/repo_health.yml

@@ -21,3 +21,6 @@ jobs:
 
       - name: Repo health gate (full)
         run: python3 scripts/repo_health.py
+
+      - name: Verify generated agent navigation artifacts are fresh
+        run: python3 scripts/refresh_agent_navigation.py --check

AGENTS.md

@@ -1,197 +1,50 @@
-# CodeContextBench Operations Guide
-
-This file is the operational quick-reference for benchmark maintenance.
-`CLAUDE.md` mirrors this file.
-
-## Benchmark Overview
-8 SDLC phase suites + 10 MCP-unique suites. SDLC tasks measure code quality
-across phases: build, debug, design, document, fix, secure, test, understand.
-MCP-unique tasks measure org-scale cross-repo discovery and retrieval.
-See `README.md` for the full suite table and `docs/TASK_CATALOG.md` for
-per-task details. See `docs/MCP_UNIQUE_TASKS.md` for the MCP-unique extension.
-
-## Canonical References
-- `README.md` - repo overview and quick start
-- `docs/CONFIGS.md` - config matrix and MCP behavior
-- `docs/QA_PROCESS.md` - pre-run, run-time, post-run validation
-- `docs/ERROR_CATALOG.md` - known failures and remediation
-- `docs/TASK_SELECTION.md` - curation/difficulty policy
-- `docs/TASK_CATALOG.md` - current task inventory
-- `docs/SCORING_SEMANTICS.md` - reward/pass interpretation (incl. oracle checks + hybrid scoring)
-- `docs/EVALUATION_PIPELINE.md` - unified eval: verifier → LLM judge → statistics → report
-- `docs/RETRIEVAL_EVAL_SPEC.md` - full retrieval/IR evaluation pipeline (normalized events → metrics/probes/taxonomy artifacts)
-- `docs/MCP_UNIQUE_TASKS.md` - MCP-unique task system (suites, authoring, oracle, DS tasks)
-- `docs/MCP_UNIQUE_CALIBRATION.md` - oracle coverage analysis and threshold calibration data
-- `docs/WORKFLOW_METRICS.md` - timing/cost metric definitions
-- `docs/AGENT_INTERFACE.md` - runtime I/O contract
-- `docs/EXTENSIBILITY.md` - safe suite/task/config extension
-- `docs/REPO_HEALTH.md` - health gate and branch hygiene (reduce drift)
-- `docs/LEADERBOARD.md` - ranking policy
-- `docs/SUBMISSION.md` - submission format
-- `docs/SKILLS.md` - AI agent skill system overview
-- `skills/` - operational runbooks for AI agents (see `skills/README.md`)
-
-## Git Policy
-- **All work happens on `main`** — do NOT create feature branches.
-- Never run `git checkout -b` or `git switch -c`.
-- Commit directly to `main`. This avoids cross-session branch confusion when multiple agents work on the repo.
-
-## Run Launch Policy
-- **Every `harbor run` invocation MUST be gated by interactive confirmation.**
-  The user must see a pre-flight summary and press Enter before any benchmark
-  task launches. There is no `--yes` or unattended mode.
-- Use `confirm_launch "description" "config" N` from `_common.sh` in one-off
-  scripts. `run_selected_tasks.sh` has its own built-in pre-flight gate.
-- **Never write a script that calls `harbor run` without a confirmation gate.**
-- **Never pass `--yes` to `run_selected_tasks.sh`** — the flag has been removed.
-
-## Typical Skill Routing
-Use these defaults unless there is a task-specific reason not to.
-
-- **Before commit or push:** `repo-health` — run `python3 scripts/repo_health.py` (or `--quick` if only docs/config changed). Do not commit/push with failing health checks.
-- Pre-run readiness: `check-infra`, `validate-tasks`
-- Launch/runs: `run-benchmark`, `run-status`, `watch-benchmarks`
-- Failure investigation: `triage-failure`, `quick-rerun`
-- Cross-config analysis: `compare-configs`, `mcp-audit`, `ir-analysis`
-- Cost/reporting: `cost-report`, `generate-report`
-- Data hygiene: `sync-metadata`, `reextract-metrics`, `archive-run`
-- Planning/prioritization: `whats-next`
-
-## Evaluation Configs
-Config names encode three dimensions: `{agent}-{source}-{verifier}`.
-
-**SDLC suites** (`ccb_build`, `ccb_debug`, etc.): use **baseline-local-direct**
-+ **mcp-remote-direct**. Agent produces code changes; verifier checks git diffs.
-
-**MCP-unique suites** (`ccb_mcp_*`): use **baseline-local-artifact** +
-**mcp-remote-artifact**. Agent produces `answer.json`; verifier scores against
-oracle. Never use `-direct` configs for MCP-unique suites.
-
-MCP configs use `Dockerfile.sg_only` (direct) or `Dockerfile.artifact_only`
-(artifact) so the agent must discover code via MCP tools. The verifier clones
-the mirror repo at verification time and overlays agent changes before scoring.
-See `docs/CONFIGS.md` for the full config matrix.
-
-## Standard Workflow
-0. **Before commit or push:** Run `python3 scripts/repo_health.py` (or `--quick`). Fix any failures so main stays clean and drift is caught early (see `docs/REPO_HEALTH.md`).
-1. Run infrastructure checks before any batch.
-2. Validate task integrity before launch (include runtime smoke for new/changed tasks).
-3. Run the benchmark config (`configs/*_2config.sh` or equivalent).
-4. Monitor progress and classify errors while tasks are running.
-5. Validate outputs after each batch (`result.json`, `flagged_tasks.json`, trajectory coverage).
-6. Triage failures before rerunning; avoid blind reruns.
-7. Regenerate `MANIFEST.json` and evaluation report after run completion.
-8. Sync metadata if task definitions changed.
-
-## Quality Gates
-A run is considered healthy only if all are true:
-
-- No infra blockers (tokens, Docker, disk, credentials)
-- No unexpected missing `result.json`
-- Errored tasks are classified and actionable
-- Zero-reward clusters are explained (task difficulty vs infra/tooling)
-- Trajectory gaps are accounted for (or JSONL fallback noted)
-- Config comparisons are based on matched task sets
-
-## Run Hygiene
-- Prefer isolated, well-scoped reruns (don't mix unrelated fixes in one batch).
-- Use parallel mode only when multi-account token state is confirmed fresh.
-- Keep run naming and suite/config metadata consistent.
-- Do not treat archived or draft analyses as canonical docs.
-- Keep `docs/` focused on maintained operational guidance.
-
-## Escalation Rules
-- Repeated infra failures: stop batch reruns and fix root cause first.
-- Suspected verifier bug: quarantine task, document evidence, and open follow-up.
-- Missing trajectories: use transcript fallback and record the limitation.
-- Widespread MCP regressions: run MCP usage audit before changing prompts/configs.
-
-## High-Use Commands
+# CodeContextBench Agent Router
+
+This file is the root entrypoint for AI agents working in this repository.
+Keep it small. Use it to route to the right workflow and local guide, not as the
+full operations manual.
+
+## Non-Negotiables
+- All work happens on `main`. Do not create feature branches.
+- Every `harbor run` must be gated by interactive confirmation.
+- Before commit/push, run `python3 scripts/repo_health.py` (or `--quick` for docs/config-only changes).
+
+## Minimal Loading Policy
+- Default load order: this file + one relevant skill + one relevant doc.
+- Do not open broad catalogs (`docs/TASK_CATALOG.md`, large script lists, full reports) unless required.
+- Prefer directory-local `AGENTS.md` / `CLAUDE.md` when working under `scripts/`, `configs/`, `tasks/`, or `docs/`.
+
+## Fast Routing By Intent
+- Launch or rerun benchmarks: `docs/START_HERE_BY_TASK.md` -> "Launch / Rerun Benchmarks"
+- Monitor / status: `docs/START_HERE_BY_TASK.md` -> "Monitor Active Runs"
+- Triage failures: `docs/START_HERE_BY_TASK.md` -> "Triage Failed Tasks"
+- Compare configs / MCP impact / IR: `docs/START_HERE_BY_TASK.md` -> "Analyze Results"
+- Repo policy / health gate: `docs/REPO_HEALTH.md`, `docs/ops/WORKFLOWS.md`
+- Script discovery: `docs/ops/SCRIPT_INDEX.md`
+
+## Local Guides
+- `scripts/AGENTS.md` - script categories, safe usage, one-off handling
+- `configs/AGENTS.md` - run launcher wrappers and confirmation gate policy
+- `tasks/AGENTS.md` - task metadata and validation workflow
+- `docs/AGENTS.md` - documentation IA and canonical vs archive guidance
+
+## Compaction / Handoff Checkpoints
+- Compact after exploration, before multi-file edits.
+- Compact after launching a benchmark batch.
+- Compact after completing a triage batch or report generation pass.
+- Use `docs/ops/HANDOFF_TEMPLATE.md` when handing work to a new session.
+
+## Canonical Maps
+- `docs/START_HERE_BY_TASK.md` - task-based read order
+- `docs/ops/WORKFLOWS.md` - operational workflow summaries
+- `docs/ops/TROUBLESHOOTING.md` - escalation and common failure routing
+- `docs/ops/SCRIPT_INDEX.md` - generated script registry index
+- `docs/reference/README.md` - stable specs and reference docs
+- `docs/explanations/README.md` - rationale and context docs
+
+## Maintenance
+- Root and local `AGENTS.md` / `CLAUDE.md` files are generated from sources in `docs/ops/`.
+- Regenerate after edits (single command):
 ```bash
-python3 scripts/check_infra.py
-python3 scripts/validate_tasks_preflight.py --all
-python3 scripts/validate_tasks_preflight.py --task <task_dir> --smoke-runtime
-python3 scripts/validate_task_run.py --run <run_dir>
-python3 scripts/aggregate_status.py --staging
-python3 scripts/compare_configs.py --run <run_dir>
-python3 scripts/mcp_audit.py --run <run_dir>
-python3 scripts/cost_report.py --run <run_dir>
-python3 scripts/generate_manifest.py
-python3 scripts/generate_eval_report.py
-python3 scripts/abc_audit.py --suite <suite>        # quality audit
-python3 scripts/abc_score_task.py --suite <suite>    # per-task quality score
-python3 scripts/docs_consistency_check.py            # documentation drift guard
-python3 scripts/repo_health.py                      # repo health gate (before push); --quick for fast check
+python3 scripts/refresh_agent_navigation.py
 ```
-
-## Script Entrypoints
-- `configs/_common.sh` - shared run infra (parallelism, token refresh, validation hooks, `confirm_launch()`, `validate_config_name()`)
-- `configs/sdlc_suite_2config.sh` - generic SDLC runner (used by phase wrappers)
-- `configs/{build,debug,design,document,fix,secure,test}_2config.sh` - thin SDLC phase wrappers
-- `configs/run_selected_tasks.sh` - unified runner from `selected_benchmark_tasks.json`
-- `configs/validate_one_per_benchmark.sh --smoke-runtime` - quick no-agent runtime smoke (1 task per suite)
-  - Smoke interpretation: `smoke_verifier_nonzero_with_reward` is acceptable in no-agent mode.
-  - Timeout diagnostics: `smoke_build_timeout` (image build phase) vs `smoke_verify_timeout` (verifier phase).
-- `scripts/promote_run.py` - staging to official promotion flow
-
-## Script Categories
-
-### Core Operations (used in every run)
-- `check_infra.py` - infrastructure readiness checker
-- `validate_tasks_preflight.py` - pre-flight task validation (static + optional runtime smoke)
-- `aggregate_status.py` - run scanner, status classification, watch mode
-- `validate_task_run.py` - post-run output validation
-- `status_fingerprints.py` - error classification (12 regex patterns)
-- `generate_eval_report.py` - deterministic evaluation report generator
-- `generate_manifest.py` - rebuild MANIFEST from on-disk results
-
-### Analysis & Comparison
-- `compare_configs.py` - cross-config divergence analysis
-- `mcp_audit.py` - MCP tool usage audit
-- `ir_analysis.py` - information retrieval analysis
-- `cost_report.py` - token/cost aggregation
-- `cost_breakdown_analysis.py` - detailed cost breakdown
-- `failure_analysis.py` - failure pattern analysis
-- `reliability_analysis.py` - reliability metrics
-- `audit_traces.py` - agent trace auditing
-- `ds_audit.py` - Deep Search usage audit
-
-### Repo health (reduce drift, clean branches)
-- `repo_health.py` - single gate: docs consistency + selection file + task preflight (see docs/REPO_HEALTH.md)
-- `docs_consistency_check.py` - documentation drift guard
-
-### Quality Assurance
-- `abc_audit.py` - ABC benchmark quality audit (32 criteria across 3 dimensions)
-- `abc_score_task.py` - per-task quality scoring
-- `abc_criteria.py` - ABC criteria data model
-- `validate_official_integrity.py` - official run integrity checks
-- `quarantine_invalid_tasks.py` - quarantine tasks with zero MCP usage
-
-### Data Management
-- `sync_task_metadata.py` - task.toml vs registry reconciliation (--fix to auto-update)
-- `archive_run.py` - archive old runs to save disk
-- `rerun_failed.py` - generate rerun commands for failed tasks
-- `promote_run.py` - staging to official promotion flow
-- `extract_task_metrics.py` - per-task metric extraction
-- `reextract_all_metrics.py` - bulk re-extraction
-
-### Submission & Reporting
-- `validate_submission.py` - validate submission format
-- `package_submission.py` - package submission archive
-- `generate_leaderboard.py` - generate leaderboard rankings
-- `generate_comprehensive_report.py` - comprehensive analysis report
-- `ingest_judge_results.py` - ingest LLM judge results
-
-### Task Creation & Selection
-- `select_benchmark_tasks.py` - canonical task selection pipeline
-- `mine_bug_tasks.py` - mine GitHub for bug-fix tasks
-- `generate_pytorch_expected_diffs.py` - generate PyTorch ground truth diffs
-
-### One-Off / Historical
-Scripts in `scripts/` prefixed with `rerun_`, `backfill_`, `fix_`, or `repair_`
-are one-off scripts used to address specific past issues. They are preserved
-for auditability but are not part of the standard workflow.
-
-DependEval-specific scripts (`dependeval_eval_*.py`, `generate_dependeval_tasks.py`,
-`select_dependeval_tasks.py`, `materialize_dependeval_repos.py`) relate to the
-archived ccb_dependeval suite.