test: destroy 9 config-schema.cjs/core.cjs source-grep tests, replace with behavioral config-set (#2696)

* test: destroy 9 config-schema.cjs/core.cjs source-grep tests, add behavioral config-set tests (#2691, #2693)

Replace source-grep theater with config-set behavioral tests:
- execute-phase-wave: config-set workflow.use_worktrees replaces VALID_CONFIG_KEYS grep
- inline-plan-threshold: delete redundant source-grep (behavioral test at L36 already covered it)
- plan-bounce: config-set for plan_bounce / plan_bounce_script / plan_bounce_passes replaces 3 key-presence greps
- code-review: config-set for code_review / code_review_depth replaces 2 greps; removes CONFIG_PATH constant
- thinking-partner: config-set features.thinking_partner replaces two greps (config-schema.cjs AND core.cjs)

Behavioral tests survive refactors (no path constants, no file reads). The config-schema.cjs →
core.cjs migration commit 990c3e64 happened because these tests groped source paths.

Add allow-test-rule: source-text-is-the-product annotations to legitimate product-content tests:
autonomous-allowed-tools, agent-frontmatter, agent-skills-awareness, bug-2334, bug-2346,
execute-phase-wave (MD reads), plan-bounce (workflow reads). Annotations explain WHY text
inspection is the right level of testing for AI instruction files.

Closes #2691
Closes #2693

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

* test: address CodeRabbit findings on #2696

- agent-frontmatter.test.cjs: move allow-test-rule annotation from block comment
  to standalone // line comment so rule scanners can detect it
- thinking-partner.test.cjs: strengthen config-set test with config-get read-back
  assertion to verify the value was persisted, not just accepted (exit 0)

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

* test: tighten thinking_partner config assertion per CodeRabbit (#2696)

Replace config-get output substring check (includes('true') false-positive
risk) with a direct JSON read of .planning/config.json, asserting the
exact persisted value via strictEqual. This also validates the config file
was created, catching silent key-acceptance without persistence.

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

---------

Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>

tests/agent-frontmatter.test.cjs

@@ -1,3 +1,7 @@
+// allow-test-rule: source-text-is-the-product
+// Agent .md files are the installed AI agents — their frontmatter and body text IS what
+// Claude Code loads at runtime. Checking text content IS checking the deployed contract.
+
 /**
  * GSD Agent Frontmatter Tests
  *

tests/agent-skills-awareness.test.cjs

@@ -1,3 +1,6 @@
+// allow-test-rule: source-text-is-the-product
+// Agent .md files are the installed AI agents — the "Project skills" block IS the deployed
+// instruction. Checking text content IS checking what runs in production.
 'use strict';
 
 const { describe, test } = require('node:test');

tests/autonomous-allowed-tools.test.cjs

@@ -12,6 +12,9 @@ const assert = require('node:assert/strict');
 const fs = require('fs');
 const path = require('path');
 
+// allow-test-rule: source-text-is-the-product
+// commands/gsd/autonomous.md is the installed command — its frontmatter is what Claude Code
+// reads at runtime to enforce allowed-tools. Checking text content IS checking the contract.
 describe('commands/gsd/autonomous.md allowed-tools', () => {
   test('includes Agent in allowed-tools list', () => {
     const filePath = path.join(__dirname, '..', 'commands', 'gsd', 'autonomous.md');

tests/bug-2334-quick-gsd-sdk-preflight.test.cjs

@@ -19,6 +19,9 @@ const path = require('path');
 
 const WORKFLOW_PATH = path.join(__dirname, '..', 'get-shit-done', 'workflows', 'quick.md');
 
+// allow-test-rule: source-text-is-the-product
+// quick.md is the AI instruction workflow — the `command -v gsd-sdk` guard IS the fix.
+// There is no behavioral equivalent: the check runs inside the AI agent, not in gsd-tools.
 describe('bug #2334: quick workflow gsd-sdk pre-flight check', () => {
   let content;
 

tests/bug-2346-agent-read-loop-guards.test.cjs

@@ -21,6 +21,9 @@ const path = require('path');
 
 const AGENTS_DIR = path.join(__dirname, '..', 'agents');
 
+// allow-test-rule: source-text-is-the-product
+// The <critical_rules> block in agent .md files IS the fix — it is the AI instruction that
+// prevents unbounded Read loops. There is no behavioral equivalent without a live LLM run.
 describe('bug #2346: agent read loop guards', () => {
 
   describe('gsd-ui-checker', () => {

tests/code-review.test.cjs

@@ -28,7 +28,6 @@ const { runGsdTools, createTempProject, cleanup } = require('./helpers.cjs');
 const AGENTS_DIR = path.join(__dirname, '..', 'agents');
 const COMMANDS_DIR = path.join(__dirname, '..', 'commands', 'gsd');
 const WORKFLOWS_DIR = path.join(__dirname, '..', 'get-shit-done', 'workflows');
-const CONFIG_PATH = path.join(__dirname, '..', 'get-shit-done', 'bin', 'lib', 'config-schema.cjs');
 
 // Plugin directory resolution (cross-platform safe)
 const PLUGIN_WORKFLOWS_DIR = process.env.GSD_PLUGIN_ROOT || path.join(os.homedir(), '.claude', 'get-shit-done', 'workflows');
@@ -271,18 +270,24 @@ describe('CR-WORKFLOW: code review workflow structure', () => {
 // --- CR-CONFIG: config key registration ---
 
 describe('CR-CONFIG: config key registration', () => {
-  test('config.cjs contains workflow.code_review key', () => {
-    const content = fs.readFileSync(CONFIG_PATH, 'utf-8');
-
-    assert.ok(content.includes('workflow.code_review'),
-      'config.cjs missing workflow.code_review key registration');
+  test('config-set accepts workflow.code_review', () => {
+    const tmpDir = createTempProject();
+    try {
+      const result = runGsdTools('config-set workflow.code_review true', tmpDir);
+      assert.ok(result.success, `config-set should accept workflow.code_review: ${result.error}`);
+    } finally {
+      cleanup(tmpDir);
+    }
   });
 
-  test('config.cjs contains workflow.code_review_depth key', () => {
-    const content = fs.readFileSync(CONFIG_PATH, 'utf-8');
-
-    assert.ok(content.includes('workflow.code_review_depth'),
-      'config.cjs missing workflow.code_review_depth key registration');
+  test('config-set accepts workflow.code_review_depth', () => {
+    const tmpDir = createTempProject();
+    try {
+      const result = runGsdTools('config-set workflow.code_review_depth standard', tmpDir);
+      assert.ok(result.success, `config-set should accept workflow.code_review_depth: ${result.error}`);
+    } finally {
+      cleanup(tmpDir);
+    }
   });
 
   test('gsd-tools config-get workflow.code_review succeeds', () => {

tests/execute-phase-wave.test.cjs

@@ -12,12 +12,17 @@ const { test, describe } = require('node:test');
 const assert = require('node:assert/strict');
 const fs = require('fs');
 const path = require('path');
+const { runGsdTools, createTempProject, cleanup } = require('./helpers.cjs');
 
 const COMMAND_PATH = path.join(__dirname, '..', 'commands', 'gsd', 'execute-phase.md');
 const WORKFLOW_PATH = path.join(__dirname, '..', 'get-shit-done', 'workflows', 'execute-phase.md');
 const COMMANDS_DOC_PATH = path.join(__dirname, '..', 'docs', 'COMMANDS.md');
 const HELP_PATH = path.join(__dirname, '..', 'get-shit-done', 'workflows', 'help.md');
 
+// allow-test-rule: source-text-is-the-product
+// The workflow and command .md files are the installed AI instructions — their text content
+// IS what executes. String presence tests guard against accidental deletion of critical clauses.
+// See #2692 for the missing behavioral test for --wave N argument parsing.
 describe('execute-phase command: --wave flag', () => {
   test('command file exists', () => {
     assert.ok(fs.existsSync(COMMAND_PATH), 'commands/gsd/execute-phase.md should exist');
@@ -128,7 +133,6 @@ describe('use_worktrees config: cross-workflow structural coverage', () => {
   const DIAGNOSE_PATH = path.join(__dirname, '..', 'get-shit-done', 'workflows', 'diagnose-issues.md');
   const EXECUTE_PLAN_PATH = path.join(__dirname, '..', 'get-shit-done', 'workflows', 'execute-plan.md');
   const PLANNING_CONFIG_PATH = path.join(__dirname, '..', 'get-shit-done', 'references', 'planning-config.md');
-  const CONFIG_CJS_PATH = path.join(__dirname, '..', 'get-shit-done', 'bin', 'lib', 'config-schema.cjs');
 
   test('quick workflow reads USE_WORKTREES from config', () => {
     const content = fs.readFileSync(QUICK_PATH, 'utf-8');
@@ -174,11 +178,14 @@ describe('use_worktrees config: cross-workflow structural coverage', () => {
     );
   });
 
-  test('config.cjs includes workflow.use_worktrees in VALID_CONFIG_KEYS', () => {
-    const content = fs.readFileSync(CONFIG_CJS_PATH, 'utf-8');
-    assert.ok(
-      content.includes("'workflow.use_worktrees'"),
-      'config.cjs VALID_CONFIG_KEYS should include workflow.use_worktrees'
-    );
+  test('config-set accepts workflow.use_worktrees', () => {
+    // allow-test-rule: behavioral — exercises config-set validation, not source text
+    const tmpDir = createTempProject();
+    try {
+      const result = runGsdTools('config-set workflow.use_worktrees true', tmpDir);
+      assert.ok(result.success, `config-set should accept workflow.use_worktrees: ${result.error}`);
+    } finally {
+      cleanup(tmpDir);
+    }
   });
 });

tests/inline-plan-threshold.test.cjs

@@ -20,7 +20,6 @@ const { runGsdTools, createTempProject, cleanup } = require('./helpers.cjs');
 const repoRoot = path.resolve(__dirname, '..');
 const executePlanPath = path.join(repoRoot, 'get-shit-done', 'workflows', 'execute-plan.md');
 const planningConfigPath = path.join(repoRoot, 'get-shit-done', 'references', 'planning-config.md');
-const configCjsPath = path.join(repoRoot, 'get-shit-done', 'bin', 'lib', 'config-schema.cjs');
 
 describe('inline_plan_threshold config key (#1979)', () => {
   let tmpDir;
@@ -43,15 +42,6 @@ describe('inline_plan_threshold config key (#1979)', () => {
     assert.ok(result.success, `config-set should accept 0: ${result.error}`);
   });
 
-  test('VALID_CONFIG_KEYS in config.cjs contains workflow.inline_plan_threshold', () => {
-    const content = fs.readFileSync(configCjsPath, 'utf-8');
-    assert.match(
-      content,
-      /['"]workflow\.inline_plan_threshold['"]/,
-      'workflow.inline_plan_threshold must be in VALID_CONFIG_KEYS'
-    );
-  });
-
   test('planning-config.md documents workflow.inline_plan_threshold', () => {
     const content = fs.readFileSync(planningConfigPath, 'utf-8');
     assert.match(

tests/plan-bounce.test.cjs

@@ -15,35 +15,41 @@ const { test, describe } = require('node:test');
 const assert = require('node:assert/strict');
 const fs = require('fs');
 const path = require('path');
+const { runGsdTools, createTempProject, cleanup } = require('./helpers.cjs');
 
 const GSD_ROOT = path.join(__dirname, '..', 'get-shit-done');
-const CONFIG_CJS_PATH = path.join(GSD_ROOT, 'bin', 'lib', 'config-schema.cjs');
 const CONFIG_TEMPLATE_PATH = path.join(GSD_ROOT, 'templates', 'config.json');
 const PLAN_PHASE_PATH = path.join(GSD_ROOT, 'workflows', 'plan-phase.md');
 
 describe('Plan Bounce: config keys', () => {
-  test('workflow.plan_bounce is in VALID_CONFIG_KEYS', () => {
-    const content = fs.readFileSync(CONFIG_CJS_PATH, 'utf-8');
-    assert.ok(
-      content.includes("'workflow.plan_bounce'"),
-      'VALID_CONFIG_KEYS should contain workflow.plan_bounce'
-    );
+  test('config-set accepts workflow.plan_bounce', () => {
+    const tmpDir = createTempProject();
+    try {
+      const result = runGsdTools('config-set workflow.plan_bounce true', tmpDir);
+      assert.ok(result.success, `config-set should accept workflow.plan_bounce: ${result.error}`);
+    } finally {
+      cleanup(tmpDir);
+    }
   });
 
-  test('workflow.plan_bounce_script is in VALID_CONFIG_KEYS', () => {
-    const content = fs.readFileSync(CONFIG_CJS_PATH, 'utf-8');
-    assert.ok(
-      content.includes("'workflow.plan_bounce_script'"),
-      'VALID_CONFIG_KEYS should contain workflow.plan_bounce_script'
-    );
+  test('config-set accepts workflow.plan_bounce_script', () => {
+    const tmpDir = createTempProject();
+    try {
+      const result = runGsdTools('config-set workflow.plan_bounce_script ./bounce.sh', tmpDir);
+      assert.ok(result.success, `config-set should accept workflow.plan_bounce_script: ${result.error}`);
+    } finally {
+      cleanup(tmpDir);
+    }
   });
 
-  test('workflow.plan_bounce_passes is in VALID_CONFIG_KEYS', () => {
-    const content = fs.readFileSync(CONFIG_CJS_PATH, 'utf-8');
-    assert.ok(
-      content.includes("'workflow.plan_bounce_passes'"),
-      'VALID_CONFIG_KEYS should contain workflow.plan_bounce_passes'
-    );
+  test('config-set accepts workflow.plan_bounce_passes', () => {
+    const tmpDir = createTempProject();
+    try {
+      const result = runGsdTools('config-set workflow.plan_bounce_passes 2', tmpDir);
+      assert.ok(result.success, `config-set should accept workflow.plan_bounce_passes: ${result.error}`);
+    } finally {
+      cleanup(tmpDir);
+    }
   });
 });
 
@@ -76,6 +82,9 @@ describe('Plan Bounce: config template defaults', () => {
   });
 });
 
+// allow-test-rule: source-text-is-the-product
+// plan-phase.md is the installed AI workflow instruction — its text content IS what executes.
+// String presence tests guard against accidental deletion of bounce step clauses.
 describe('Plan Bounce: plan-phase.md step 12.5', () => {
   let content;
 

tests/thinking-partner.test.cjs

@@ -2,6 +2,7 @@ const { describe, test } = require('node:test');
 const assert = require('node:assert/strict');
 const fs = require('fs');
 const path = require('path');
+const { runGsdTools, createTempProject, cleanup } = require('./helpers.cjs');
 
 const GSD_ROOT = path.join(__dirname, '..', 'get-shit-done');
 
@@ -66,27 +67,24 @@ describe('Thinking Partner Integration (#1726)', () => {
 
   // Config tests
   describe('Config integration', () => {
-    test('features.thinking_partner is in VALID_CONFIG_KEYS', () => {
-      const configSrc = fs.readFileSync(
-        path.join(GSD_ROOT, 'bin', 'lib', 'config-schema.cjs'),
-        'utf-8'
-      );
-      assert.ok(
-        configSrc.includes("'features.thinking_partner'"),
-        'VALID_CONFIG_KEYS should contain features.thinking_partner'
-      );
-    });
-
-    test('features is in KNOWN_TOP_LEVEL section containers', () => {
-      const coreSrc = fs.readFileSync(
-        path.join(GSD_ROOT, 'bin', 'lib', 'core.cjs'),
-        'utf-8'
-      );
-      // The KNOWN_TOP_LEVEL set should include 'features' in section containers
-      assert.ok(
-        coreSrc.includes("'features'"),
-        'KNOWN_TOP_LEVEL should contain features as a section container'
-      );
+    test('config-set accepts features.thinking_partner', () => {
+      // Exercises VALID_CONFIG_KEYS membership and KNOWN_TOP_LEVEL acceptance in one call.
+      // Replaces two source-grep tests that read config-schema.cjs and core.cjs (see #2691).
+      const tmpDir = createTempProject();
+      try {
+        const setResult = runGsdTools('config-set features.thinking_partner true', tmpDir);
+        assert.ok(setResult.success, `config-set should accept features.thinking_partner: ${setResult.error}`);
+        const configPath = path.join(tmpDir, '.planning', 'config.json');
+        assert.ok(fs.existsSync(configPath), 'config-set should create .planning/config.json');
+        const config = JSON.parse(fs.readFileSync(configPath, 'utf-8'));
+        assert.strictEqual(
+          config.features?.thinking_partner,
+          true,
+          'config-set should persist features.thinking_partner=true'
+        );
+      } finally {
+        cleanup(tmpDir);
+      }
     });
   });