codex-genesis-harness 0.1.7 → 0.1.9

package/scripts/schema/001-init.sql

@@ -0,0 +1,129 @@
+-- Harness v0 schema — migration 001
+-- Durable layer for operational harness data.
+-- Policy docs (HARNESS.md, FEATURE_INTAKE.md, ARCHITECTURE.md) stay as
+-- human-readable references. This database stores the operational records
+-- that agents produce and query during work.
+
+PRAGMA journal_mode = WAL;
+PRAGMA foreign_keys = ON;
+
+----------------------------------------------------------------------
+-- Schema version
+----------------------------------------------------------------------
+CREATE TABLE IF NOT EXISTS schema_version (
+    version     INTEGER PRIMARY KEY,
+    applied_at  TEXT    NOT NULL DEFAULT (datetime('now'))
+);
+
+INSERT INTO schema_version (version) VALUES (1);
+
+----------------------------------------------------------------------
+-- Intake: classifying incoming work
+----------------------------------------------------------------------
+CREATE TABLE intake (
+    id            INTEGER PRIMARY KEY AUTOINCREMENT,
+    created_at    TEXT    NOT NULL DEFAULT (datetime('now')),
+    input_type    TEXT    NOT NULL
+                         CHECK(input_type IN (
+                           'new_spec','spec_slice','change_request',
+                           'new_initiative','maintenance','harness_improvement'
+                         )),
+    summary       TEXT    NOT NULL,
+    risk_lane     TEXT    NOT NULL
+                         CHECK(risk_lane IN ('tiny','normal','high_risk')),
+    risk_flags    TEXT,          -- JSON array, e.g. ["auth","data_model"]
+    affected_docs TEXT,          -- JSON array of doc paths
+    story_id      TEXT,          -- links to story.id when one is created
+    notes         TEXT
+);
+
+----------------------------------------------------------------------
+-- Story: work packets and their validation status
+-- Replaces hand-edited TEST_MATRIX.md rows.
+----------------------------------------------------------------------
+CREATE TABLE story (
+    id               TEXT PRIMARY KEY,   -- e.g. US-001
+    title            TEXT NOT NULL,
+    created_at       TEXT NOT NULL DEFAULT (datetime('now')),
+    risk_lane        TEXT NOT NULL
+                     CHECK(risk_lane IN ('tiny','normal','high_risk')),
+    contract_doc     TEXT,               -- path to product doc
+    status           TEXT NOT NULL DEFAULT 'planned'
+                     CHECK(status IN (
+                       'planned','in_progress','implemented','changed','retired'
+                     )),
+    unit_proof       INTEGER NOT NULL DEFAULT 0,
+    integration_proof INTEGER NOT NULL DEFAULT 0,
+    e2e_proof        INTEGER NOT NULL DEFAULT 0,
+    platform_proof   INTEGER NOT NULL DEFAULT 0,
+    evidence         TEXT,
+    notes            TEXT
+);
+
+----------------------------------------------------------------------
+-- Decision: durable records with optional verification
+----------------------------------------------------------------------
+CREATE TABLE decision (
+    id                    TEXT PRIMARY KEY,  -- e.g. 0001
+    title                 TEXT NOT NULL,
+    created_at            TEXT NOT NULL DEFAULT (datetime('now')),
+    status                TEXT NOT NULL DEFAULT 'proposed'
+                          CHECK(status IN (
+                            'proposed','accepted','superseded','rejected'
+                          )),
+    doc_path              TEXT,              -- path to the markdown ADR
+    verify_command        TEXT,              -- optional check command
+    last_verified_at      TEXT,
+    last_verified_result  TEXT
+                          CHECK(last_verified_result IN ('pass','fail') OR
+                                last_verified_result IS NULL),
+    predicted_impact      TEXT,
+    actual_outcome        TEXT,
+    notes                 TEXT
+);
+
+----------------------------------------------------------------------
+-- Backlog: harness improvement proposals with evidence loop
+----------------------------------------------------------------------
+CREATE TABLE backlog (
+    id                    INTEGER PRIMARY KEY AUTOINCREMENT,
+    created_at            TEXT    NOT NULL DEFAULT (datetime('now')),
+    title                 TEXT    NOT NULL,
+    discovered_while      TEXT,
+    current_pain          TEXT,
+    suggested_improvement TEXT,
+    risk                  TEXT    CHECK(risk IN ('tiny','normal','high_risk')),
+    status                TEXT    NOT NULL DEFAULT 'proposed'
+                          CHECK(status IN (
+                            'proposed','accepted','implemented','rejected'
+                          )),
+    predicted_impact      TEXT,
+    actual_outcome        TEXT,
+    implemented_at        TEXT,
+    notes                 TEXT
+);
+
+----------------------------------------------------------------------
+-- Trace: agent task execution records (observability foundation)
+----------------------------------------------------------------------
+CREATE TABLE trace (
+    id              INTEGER PRIMARY KEY AUTOINCREMENT,
+    created_at      TEXT    NOT NULL DEFAULT (datetime('now')),
+    task_summary    TEXT    NOT NULL,
+    intake_id       INTEGER REFERENCES intake(id),
+    story_id        TEXT    REFERENCES story(id),
+    agent           TEXT,
+    actions_taken   TEXT,       -- JSON array
+    files_read      TEXT,       -- JSON array
+    files_changed   TEXT,       -- JSON array
+    decisions_made  TEXT,       -- JSON array
+    errors          TEXT,       -- JSON array
+    outcome         TEXT
+                    CHECK(outcome IN (
+                      'completed','blocked','partial','failed'
+                    )),
+    duration_seconds INTEGER,
+    token_estimate   INTEGER,
+    harness_friction TEXT,
+    notes            TEXT
+);

package/scripts/schema/002-story-verify.sql

@@ -0,0 +1,9 @@
+-- Harness v0 schema - migration 002
+-- Story-level mechanical verification.
+
+ALTER TABLE story ADD COLUMN verify_command TEXT;
+ALTER TABLE story ADD COLUMN last_verified_at TEXT;
+ALTER TABLE story ADD COLUMN last_verified_result TEXT
+    CHECK(last_verified_result IN ('pass','fail') OR last_verified_result IS NULL);
+
+INSERT INTO schema_version (version) VALUES (2);

package/scripts/schema/003-tool-registry.sql

@@ -0,0 +1,15 @@
+-- Harness v0 schema - migration 003
+-- Machine-readable registry for user-provided project tools.
+
+CREATE TABLE tool (
+    name           TEXT PRIMARY KEY,
+    created_at     TEXT NOT NULL DEFAULT (datetime('now')),
+    provider       TEXT NOT NULL DEFAULT 'custom',
+    command        TEXT NOT NULL,
+    description    TEXT NOT NULL,
+    args           TEXT,
+    responsibility TEXT NOT NULL,
+    since          TEXT NOT NULL DEFAULT 'registered'
+);
+
+INSERT INTO schema_version (version) VALUES (3);

package/scripts/schema/004-intervention.sql

@@ -0,0 +1,15 @@
+-- Harness v0 schema - migration 004
+-- Review, human, CI, or agent interventions separated from normal traces.
+
+CREATE TABLE intervention (
+    id          INTEGER PRIMARY KEY AUTOINCREMENT,
+    created_at  TEXT NOT NULL DEFAULT (datetime('now')),
+    trace_id    INTEGER REFERENCES trace(id),
+    story_id    TEXT,
+    type        TEXT NOT NULL CHECK(type IN ('correction','override','escalation','approval')),
+    description TEXT NOT NULL,
+    source      TEXT NOT NULL CHECK(source IN ('human','reviewer','ci','agent')),
+    impact      TEXT
+);
+
+INSERT INTO schema_version (version) VALUES (4);

package/scripts/scratch_parser.js

@@ -0,0 +1,49 @@
+const fs = require('fs');
+const parser = require('@babel/parser');
+const traverse = require('@babel/traverse').default;
+
+const code = `
+import { something } from './my-module';
+const x = require('another-module');
+export class MyClass {}
+export function myFunc() {}
+export const myArrow = async () => {};
+`;
+
+const ast = parser.parse(code, {
+  sourceType: 'module',
+  plugins: ['typescript']
+});
+
+const exportsList = [];
+const importsList = [];
+
+traverse(ast, {
+  ExportNamedDeclaration(path) {
+    const decl = path.node.declaration;
+    if (decl) {
+      if (decl.type === 'ClassDeclaration' && decl.id) {
+        exportsList.push('class ' + decl.id.name);
+      } else if (decl.type === 'FunctionDeclaration' && decl.id) {
+        exportsList.push('function ' + decl.id.name);
+      } else if (decl.type === 'VariableDeclaration') {
+        decl.declarations.forEach(d => {
+          if (d.id) exportsList.push('const ' + d.id.name);
+        });
+      }
+    }
+  },
+  ImportDeclaration(path) {
+    importsList.push(path.node.source.value);
+  },
+  CallExpression(path) {
+    if (path.node.callee.name === 'require' && path.node.arguments.length > 0) {
+      if (path.node.arguments[0].type === 'StringLiteral') {
+        importsList.push(path.node.arguments[0].value);
+      }
+    }
+  }
+});
+
+console.log('Exports:', exportsList);
+console.log('Imports:', importsList);

package/scripts/spec_visual_sync.js

@@ -2,7 +2,7 @@
 
 /**
  * Spec Visual Sync - Bi-directional AST Sync between Mermaid ERD and JSON Contracts
- * Part of Genesis Codex Harness v0.1.7
+ * Part of Genesis Codex Harness v0.1.8
  */
 
 const fs = require('fs');

package/scripts/test_generator.js

@@ -2,7 +2,7 @@
 
 /**
  * Contract-Driven Test Auto-Generator
- * Part of Genesis Codex Harness v0.1.7
+ * Part of Genesis Codex Harness v0.1.8
  */
 
 const fs = require('fs');
@@ -62,7 +62,7 @@ const requiredFields = schema.required || Object.keys(properties);
 // Construct test cases content
 let testSuiteCode = `/**
  * Integration Test for Endpoint: /api/${endpoint}
- * Automatically generated by Genesis Contract-Driven Test Generator (v0.1.7)
+ * Automatically generated by Genesis Contract-Driven Test Generator (v0.1.8)
  * Strictly Enforces TDD Contract Compliance.
  */
 

package/scripts/transition_state.sh

@@ -1,5 +1,7 @@
 #!/bin/bash
 
+set -euo pipefail
+
 if [ -z "$1" ]; then
   echo "Usage: bash scripts/transition_state.sh <NEW_STATE> [Reason]"
   exit 1
@@ -30,14 +32,16 @@ const fs = require('fs');
 const file = '$STATE_FILE';
 const newState = '$NEW_STATE';
 const reason = '$REASON';
+const now = new Date().toISOString();
 
 const allowed = {
   'INIT': ['REQUIREMENTS_GATHERING', 'PLANNING'],
   'REQUIREMENTS_GATHERING': ['PLANNING'],
   'PLANNING': ['IMPLEMENTATION'],
   'IMPLEMENTATION': ['VERIFICATION', 'PLANNING'],
-  'VERIFICATION': ['COMPLETED', 'IMPLEMENTATION'],
-  'COMPLETED': ['INIT', 'REQUIREMENTS_GATHERING']
+  'VERIFICATION': ['RELEASE_READY', 'IMPLEMENTATION'],
+  'RELEASE_READY': ['COMPLETED', 'IMPLEMENTATION'],
+  'COMPLETED': ['INIT', 'REQUIREMENTS_GATHERING', 'IMPLEMENTATION']
 };
 
 let data = JSON.parse(fs.readFileSync(file, 'utf8'));
@@ -45,8 +49,18 @@ const current = data.current_state || 'INIT';
 
 if (allowed[current] && allowed[current].includes(newState)) {
   data.history = data.history || [];
-  data.history.push({ from: current, to: newState, reason: reason, timestamp: new Date().toISOString() });
+  data.history.push({ from: current, to: newState, reason: reason, timestamp: now, session_id: data.session_id || 'manual-transition' });
   data.current_state = newState;
+  data.session_started_at = data.session_started_at || now;
+  data.last_updated_at = now;
+  if (newState === 'COMPLETED') {
+    data.completed_at = now;
+    data.active_work = '';
+    data.pending_tasks = [];
+    data.latest_recovery_point = reason;
+  } else {
+    delete data.completed_at;
+  }
   fs.writeFileSync(file, JSON.stringify(data, null, 2));
   console.log('Transition successful: ' + current + ' -> ' + newState);
 } else {
@@ -56,11 +70,21 @@ if (allowed[current] && allowed[current].includes(newState)) {
 "
 
 if [ $? -eq 0 ]; then
-  echo "# Current State: $NEW_STATE" > "$CURRENT_STATE_MD"
-  echo "Last updated: $(date)" >> "$CURRENT_STATE_MD"
-  echo "" >> "$CURRENT_STATE_MD"
-  echo "## Reason" >> "$CURRENT_STATE_MD"
-  echo "$REASON" >> "$CURRENT_STATE_MD"
+  SESSION_ID=$(node -p "JSON.parse(require('fs').readFileSync('$STATE_FILE', 'utf8')).session_id || 'manual-transition'")
+  TTFV_SECONDS=$(node -p "JSON.parse(require('fs').readFileSync('$STATE_FILE', 'utf8')).ttfv_seconds || 0")
+  cat > "$CURRENT_STATE_MD" <<EOF
+# Current System State
+
+**Time**: $(date +%F)
+**Status**: \`$NEW_STATE\`
+**Latest Session**: \`$SESSION_ID\`
+**Time to First Verification (TTFV)**: ${TTFV_SECONDS}s
+
+## Latest Transition
+
+- State changed to \`$NEW_STATE\`
+- Reason: $REASON
+EOF
   exit 0
 else
   exit 1

package/scripts/uninstall.sh

@@ -23,6 +23,10 @@ skill_names=(
   genesis-research-first
   genesis-release
   spec-impact-engine
+  genesis-executing-plans
+  genesis-test-driven-development
+  genesis-verification-before-completion
+  genesis-using-git-worktrees
   project-genesis-harness
 )
 codex_home="${CODEX_HOME:-$HOME/.codex}"

package/scripts/validation_gates.sh

@@ -1,85 +1,7 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-echo "====================================="
-echo "   RUNNING VALIDATION GATES          "
-echo "====================================="
-
 repo_root="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
-FAILURES=0
-
-fail() {
-  echo "❌ VALIDATION FAILED: $*" >&2
-  FAILURES=$((FAILURES + 1))
-}
-
-echo "1. Checking for leftover debug logs and TODOs..."
-# Exclude node_modules, .git, .codex, scripts, .codebase, bin, and md files
-EXCLUDES="--exclude-dir=node_modules --exclude-dir=.git --exclude-dir=.codex --exclude-dir=scripts --exclude-dir=.codebase --exclude-dir=bin --exclude=*.md"
-
-# We check for TODO, FIXME, console.log, print( (python)
-# Using grep recursively
-if grep -rn $EXCLUDES -E 'TODO|FIXME|console\.log|print\(' "$repo_root" | grep -v 'validation_gates.sh'; then
-  fail "Found unresolved TODOs or leftover debug logs in codebase!"
-else
-  echo "✅ Codebase cleanliness gate passed."
-fi
-
-echo "2. Verifying Harness Integrity..."
-if [ -f "$repo_root/scripts/verify.sh" ]; then
-  if bash "$repo_root/scripts/verify.sh" > /dev/null 2>&1; then
-    echo "✅ Harness Integrity gate passed."
-  else
-    fail "verify.sh failed. Core files or templates are missing."
-  fi
-fi
-
-echo "3. Checking for Documentation Drift (Alignment with Code changes)..."
-if [ -d "$repo_root/.git" ]; then
-  # Get list of modified files in git
-  CHANGED_FILES=$(git diff --name-only HEAD 2>/dev/null || true)
-  
-  if [ -n "$CHANGED_FILES" ]; then
-    # API Drift: code under src/ modified, but API contracts not updated
-    if echo "$CHANGED_FILES" | grep -qE "src/.*api|src/.*endpoint|src/.*route" && ! echo "$CHANGED_FILES" | grep -qE "contracts/api/|.codebase/API_CONTRACTS.md|.planning/API_DOCS.md"; then
-      echo "⚠️  WARNING: You changed API code under src/ but did not update API_CONTRACTS.md, API_DOCS.md or contracts/api/!"
-    fi
-
-    # Database Drift: models or schemas modified, but DOMAIN_MODELS.md not updated
-    if echo "$CHANGED_FILES" | grep -qE "model|schema|db" && ! echo "$CHANGED_FILES" | grep -qE ".codebase/DOMAIN_MODELS.md"; then
-      echo "⚠️  WARNING: You changed database/model files but did not update DOMAIN_MODELS.md!"
-    fi
-
-    # Test Drift: test files modified, but TEST_MATRIX.md not updated
-    if echo "$CHANGED_FILES" | grep -qE "tests/|playwright/" && ! echo "$CHANGED_FILES" | grep -qE ".codebase/TEST_MATRIX.md"; then
-      echo "⚠️  WARNING: You changed test files but did not update TEST_MATRIX.md!"
-    fi
-
-    # Dependency Drift: package.json dependencies modified, but DEPENDENCY_GRAPH.md not updated
-    if echo "$CHANGED_FILES" | grep -q "package.json" && ! echo "$CHANGED_FILES" | grep -q ".codebase/DEPENDENCY_GRAPH.md"; then
-      if git diff package.json 2>/dev/null | grep -qE '^\+.*"(dependencies|devDependencies)"'; then
-        echo "⚠️  WARNING: You updated package.json dependencies but did not update DEPENDENCY_GRAPH.md!"
-      fi
-    fi
-    echo "✅ Documentation alignment check complete."
-  fi
-else
-  echo "⚠️  Git repository not found. Skipping drift check."
-fi
-
-echo "4. Running Pre-emptive Prompt Sentinel check..."
-if [ -f "$repo_root/scripts/prompt_sentinel.js" ] && [ -f "$repo_root/.codebase/CURRENT_STATE.md" ]; then
-  # Run prompt sentinel check on the state file as a pre-flight test
-  node "$repo_root/scripts/prompt_sentinel.js" --check "$repo_root/.codebase/CURRENT_STATE.md" --threshold 1500
-fi
-
-
 
-echo "====================================="
-if [ $FAILURES -gt 0 ]; then
-  echo "❌ $FAILURES Validation Gate(s) failed."
-  exit 1
-else
-  echo "✅ All Validation Gates passed! Output is ready for production."
-  exit 0
-fi
+echo "Running canonical Genesis verification gate..."
+exec node "$repo_root/bin/genesis-harness.js" verify-gate

package/scripts/verify.sh

@@ -25,6 +25,10 @@ skill_names=(
   genesis-research-first
   genesis-release
   spec-impact-engine
+  genesis-executing-plans
+  genesis-test-driven-development
+  genesis-verification-before-completion
+  genesis-using-git-worktrees
 )
 
 required_memory_files=(
@@ -51,7 +55,7 @@ required_context_files=(
 )
 
 required_contract_roots=(api agents events ui)
-required_fixture_roots=(api agents pipeline render tts images videos)
+required_fixture_roots=(api agents pipeline render images)
 required_test_roots=(contracts integration unit fixtures)
 required_playwright_roots=(e2e smoke visual fixtures)
 required_observability_roots=(agent-runs failures decision-logs)
@@ -117,7 +121,14 @@ required_scripts=(
   run-verify-loop.sh
 )
 
+max_skill_lines=500
+
 fail() {
+  if [ "${VIBE_MODE:-0}" = "1" ]; then
+    echo "verify WARN (VIBE_MODE): $*" >&2
+    echo "- [$(date -u +"%Y-%m-%dT%H:%M:%SZ")] VIBE_MODE Bypass: Verify check failed - $*" >> "$repo_root/.codebase/TECH_DEBT.md"
+    return 0
+  fi
   echo "verify failed: $*" >&2
   exit 1
 }
@@ -169,12 +180,17 @@ verify_repository_harness() {
 
 verify_repository_harness
 
+node "$repo_root/scripts/check-repository-hygiene.js"
+
 verify_skill_metadata() {
   local skill_dir="$1"
   local expected_name="$2"
+  local skill_lines
 
   [ -f "$skill_dir/SKILL.md" ] || fail "missing SKILL.md: $skill_dir"
   [ -f "$skill_dir/agents/openai.yaml" ] || fail "missing agents/openai.yaml: $skill_dir"
+  skill_lines="$(wc -l < "$skill_dir/SKILL.md" | tr -d ' ')"
+  [ "$skill_lines" -le "$max_skill_lines" ] || fail "SKILL.md exceeds ${max_skill_lines} lines ($skill_lines): $skill_dir"
   grep -q "^name: $expected_name[[:space:]]*$" "$skill_dir/SKILL.md" || fail "invalid skill name frontmatter (expected 'name: $expected_name'): $skill_dir"
   grep -q '^description:' "$skill_dir/SKILL.md" || fail "missing description frontmatter: $skill_dir"
   grep -q 'default_prompt:' "$skill_dir/agents/openai.yaml" || fail "missing default_prompt: $skill_dir"
@@ -246,6 +262,7 @@ verify_minimal_skill() {
   local skill_dir="$1"
 
   [ -d "$skill_dir/templates" ] || fail "missing templates/: $skill_dir"
+  [ -d "$skill_dir/checklists" ] || fail "missing checklists/: $skill_dir"
   [ -d "$skill_dir/examples" ] || fail "missing examples/: $skill_dir"
 }
 
@@ -264,7 +281,7 @@ verify_one() {
     genesis-new-design|genesis-upgrade-design)
       verify_design_skill "$skill_dir" "$dir_name"
       ;;
-    genesis-architecture|genesis-planning|genesis-codebase-map|genesis-design-spec|genesis-api-contract|genesis-ui-ux-test|genesis-harness-engineering|genesis-ai-provider|genesis-pipeline-orchestration|genesis-api-sync)
+    genesis-architecture|genesis-planning|genesis-codebase-map|genesis-design-spec|genesis-api-contract|genesis-ui-ux-test|genesis-harness-engineering|genesis-ai-provider|genesis-pipeline-orchestration|genesis-api-sync|genesis-executing-plans|genesis-test-driven-development|genesis-verification-before-completion|genesis-using-git-worktrees)
       verify_skill_metadata "$skill_dir" "$dir_name"
       verify_skill_protocol "$skill_dir"
       ;;

package/tests/fixtures/fixture-index.md

@@ -2,3 +2,8 @@
 
 Map every fixture to the contract, test, and module it validates.
 
+| Fixture | Validates | Test / Module |
+|---|---|---|
+| `fixtures/pipeline/run-to-feature-execution-fixture.md` | `run --idea` advances from discovery into active feature execution with resumable artifacts plus typed API/UI contract scaffolding | `tests/integration/cli-smoke.test.js`, `bin/genesis-harness.js` |
+| `fixtures/pipeline/feature-completion-fixture.md` | `next` and `complete-feature` close an active feature only after executable verification and explicit evidence | `tests/integration/cli-smoke.test.js`, `bin/genesis-harness.js` |
+| `fixtures/pipeline/end-to-end-project-lifecycle-fixture.md` | Multi-feature promotion, project-wide verification, release-ready handoff, idempotent completion, event history, and pipeline audit | `tests/integration/cli-smoke.test.js`, `bin/genesis-harness.js` |