@organon-methodology/tools 0.3.0

package/dist/core/validate-workflow.test.js

@@ -0,0 +1,205 @@
+import { describe, it, expect } from 'vitest';
+import { validateWorkflow } from './validate-workflow.js';
+import { MemoryFileSystem, makeWorkflow } from './test-helpers.js';
+function makeConfig(projectRoot) {
+    return {
+        projectRoot,
+        organonPaths: ['.'],
+        organonGlobs: ['**/ETHOS.md'],
+        ignorePatterns: [],
+        workflowPaths: { generic: 'workflows' },
+        freshnessThresholdHours: 24,
+    };
+}
+describe('validateWorkflow', () => {
+    it('passes for a well-formed workflow', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/workflows/test.md': makeWorkflow(),
+            '/project/ETHOS.md': '# ethos',
+        });
+        const config = makeConfig('/project');
+        const result = await validateWorkflow({ projectRoot: '/project', config, fs });
+        expect(result.success).toBe(true);
+        expect(result.workflowsChecked).toBe(1);
+        expect(result.workflowsWithErrors).toBe(0);
+    });
+    it('succeeds when no workflow files exist', async () => {
+        const fs = new MemoryFileSystem({});
+        const config = makeConfig('/project');
+        const result = await validateWorkflow({ projectRoot: '/project', config, fs });
+        expect(result.success).toBe(true);
+        expect(result.workflowsChecked).toBe(0);
+    });
+    it('reports error when protocol_id is missing', async () => {
+        const content = makeWorkflow().replace(/protocol_id: .*\n/, '');
+        const fs = new MemoryFileSystem({
+            '/project/workflows/test.md': content,
+            '/project/ETHOS.md': '# ethos',
+        });
+        const config = makeConfig('/project');
+        const result = await validateWorkflow({ projectRoot: '/project', config, fs });
+        expect(result.errors).toContainEqual(expect.objectContaining({ code: 'WORKFLOW_MISSING_PROTOCOL_ID' }));
+    });
+    it('reports error when protocol_file is missing', async () => {
+        const content = makeWorkflow().replace(/protocol_file: .*\n/, '');
+        const fs = new MemoryFileSystem({
+            '/project/workflows/test.md': content,
+            '/project/ETHOS.md': '# ethos',
+        });
+        const config = makeConfig('/project');
+        const result = await validateWorkflow({ projectRoot: '/project', config, fs });
+        expect(result.errors).toContainEqual(expect.objectContaining({ code: 'WORKFLOW_MISSING_PROTOCOL_FILE' }));
+    });
+    it('reports error when tools array is missing', async () => {
+        const content = makeWorkflow().replace(/tools:\n  - tool:verify\n/, '');
+        const fs = new MemoryFileSystem({
+            '/project/workflows/test.md': content,
+            '/project/ETHOS.md': '# ethos',
+        });
+        const config = makeConfig('/project');
+        const result = await validateWorkflow({ projectRoot: '/project', config, fs });
+        expect(result.errors).toContainEqual(expect.objectContaining({ code: 'WORKFLOW_MISSING_TOOLS' }));
+    });
+    it('reports error when loads array is missing', async () => {
+        const content = makeWorkflow().replace(/loads:\n  - \/ETHOS\.md\n/, '');
+        const fs = new MemoryFileSystem({
+            '/project/workflows/test.md': content,
+        });
+        const config = makeConfig('/project');
+        const result = await validateWorkflow({ projectRoot: '/project', config, fs });
+        expect(result.errors).toContainEqual(expect.objectContaining({ code: 'WORKFLOW_MISSING_LOADS' }));
+    });
+    it('reports error when loads path does not resolve', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/workflows/test.md': makeWorkflow({ loads: ['/nonexistent.md'] }),
+        });
+        const config = makeConfig('/project');
+        const result = await validateWorkflow({ projectRoot: '/project', config, fs });
+        expect(result.errors).toContainEqual(expect.objectContaining({ code: 'WORKFLOW_BROKEN_LOADS_REF' }));
+    });
+    it('warns when error recovery section is missing', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/workflows/test.md': makeWorkflow({ includeRecovery: false }),
+            '/project/ETHOS.md': '# ethos',
+        });
+        const config = makeConfig('/project');
+        const result = await validateWorkflow({ projectRoot: '/project', config, fs });
+        expect(result.warnings).toContainEqual(expect.objectContaining({ code: 'WORKFLOW_NO_ERROR_RECOVERY' }));
+    });
+    it('warns when error recovery section has no table', async () => {
+        const content = makeWorkflow({ includeRecovery: false }) + '\n## Error Recovery\n\nJust some text, no table.\n';
+        const fs = new MemoryFileSystem({
+            '/project/workflows/test.md': content,
+            '/project/ETHOS.md': '# ethos',
+        });
+        const config = makeConfig('/project');
+        const result = await validateWorkflow({ projectRoot: '/project', config, fs });
+        expect(result.warnings).toContainEqual(expect.objectContaining({ code: 'WORKFLOW_RECOVERY_NO_TABLE' }));
+    });
+    it('warns when loads array exceeds threshold', async () => {
+        const manyLoadsPaths = Array.from({ length: 12 }, (_, i) => `/file${i}.md`);
+        const fs = new MemoryFileSystem({
+            '/project/workflows/test.md': makeWorkflow({ loads: manyLoadsPaths }),
+        });
+        // Create all the loads files so they resolve
+        for (const p of manyLoadsPaths) {
+            fs.addFile(`/project${p}`, '# content');
+        }
+        const config = makeConfig('/project');
+        const result = await validateWorkflow({ projectRoot: '/project', config, fs });
+        expect(result.warnings).toContainEqual(expect.objectContaining({ code: 'WORKFLOW_LOADS_OVERLOAD' }));
+    });
+    it('warns when a tool in tools array is not referenced in body', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/workflows/test.md': makeWorkflow({ tools: ['tool:verify', 'tool:unused'] }),
+            '/project/ETHOS.md': '# ethos',
+        });
+        const config = makeConfig('/project');
+        const result = await validateWorkflow({ projectRoot: '/project', config, fs });
+        expect(result.warnings).toContainEqual(expect.objectContaining({
+            code: 'WORKFLOW_UNREFERENCED_TOOL',
+            message: expect.stringContaining('tool:unused'),
+        }));
+    });
+    it('matches kebab-case tool ids against CLI-command form in body', async () => {
+        // Tool listed as "organon-verify" should match body text "organon verify"
+        const content = `---
+name: cli-workflow
+protocol_id: PROTO-TEST-1
+protocol_file: PROTOCOLS.md
+tools:
+  - organon-verify
+  - organon-health
+loads:
+  - /ETHOS.md
+---
+
+# Workflow
+
+## Steps
+
+1. Run \`organon verify\` to check gates.
+2. Run \`organon health\` to check score.
+
+## Error Recovery
+
+| Failure | Recovery Action |
+|---------|-----------------|
+| Fails | Fix it |
+`;
+        const fs = new MemoryFileSystem({
+            '/project/workflows/test.md': content,
+            '/project/ETHOS.md': '# ethos',
+        });
+        const config = makeConfig('/project');
+        const result = await validateWorkflow({ projectRoot: '/project', config, fs });
+        const toolWarnings = result.warnings.filter(w => w.code === 'WORKFLOW_UNREFERENCED_TOOL');
+        expect(toolWarnings).toHaveLength(0);
+    });
+    it('warns when workflow step count is less than protocol step count', async () => {
+        const protocolContent = `---
+type: procedures
+scope: domain
+name: test-protocol
+version: "1.0"
+summary: Test protocol
+token_estimate: 200
+protocols_count: 1
+protocols:
+  - id: PROTO-TEST-1
+    name: Test Protocol
+    steps: 6
+    automation_tier: automated
+    workflow: test-workflow
+    complexity: medium
+---
+
+## Steps
+1. Step one
+2. Step two
+3. Step three
+4. Step four
+5. Step five
+6. Step six
+`;
+        const fs = new MemoryFileSystem({
+            '/project/workflows/test.md': makeWorkflow({ steps: 3, protocolFile: 'PROTOCOLS.md', protocolId: 'PROTO-TEST-1' }),
+            '/project/PROTOCOLS.md': protocolContent,
+            '/project/ETHOS.md': '# ethos',
+        });
+        const config = makeConfig('/project');
+        const result = await validateWorkflow({ projectRoot: '/project', config, fs });
+        expect(result.warnings).toContainEqual(expect.objectContaining({ code: 'WORKFLOW_STEP_COUNT_LOW' }));
+    });
+    it('handles workflow files without frontmatter gracefully', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/workflows/test.md': '# No frontmatter workflow\n\nJust content.',
+        });
+        const config = makeConfig('/project');
+        const result = await validateWorkflow({ projectRoot: '/project', config, fs });
+        // Should report errors for missing required fields, not crash
+        expect(result.success).toBe(false);
+        expect(result.errors.length).toBeGreaterThan(0);
+    });
+});
+//# sourceMappingURL=validate-workflow.test.js.map

package/dist/core/validate-workflow.test.js.map

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package/dist/core/verify-tier4-tests.d.ts

@@ -0,0 +1,34 @@
+/**
+ * tier4-tests verification gate.
+ *
+ * Static analysis gate that checks whether test files with @organon-invariant
+ * annotations properly import from @organon-methodology/testing and call testInvariant().
+ *
+ * This gate does NOT run tests — that's CI's job. It only checks structure:
+ * 1. Find files with @organon-invariant annotations
+ * 2. Verify they import from @organon-methodology/testing
+ * 3. Verify they contain testInvariant() calls
+ * 4. Report gaps
+ */
+import type { DiagnosticMessage, FileSystem, OrganonConfig } from './types.js';
+export interface Tier4TestsResult {
+    success: boolean;
+    /** Test files that were scanned */
+    filesScanned: number;
+    /** Files with @organon-invariant annotations */
+    annotatedFiles: number;
+    /** Files that pass all checks */
+    validFiles: number;
+    errors: DiagnosticMessage[];
+    warnings: DiagnosticMessage[];
+}
+/**
+ * Verify that test files with @organon-invariant annotations
+ * properly use @organon-methodology/testing infrastructure.
+ */
+export declare function verifyTier4Tests(options: {
+    projectRoot: string;
+    config: OrganonConfig;
+    fs: FileSystem;
+}): Promise<Tier4TestsResult>;
+//# sourceMappingURL=verify-tier4-tests.d.ts.map

package/dist/core/verify-tier4-tests.d.ts.map

@@ -0,0 +1 @@
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package/dist/core/verify-tier4-tests.js

@@ -0,0 +1,106 @@
+/**
+ * tier4-tests verification gate.
+ *
+ * Static analysis gate that checks whether test files with @organon-invariant
+ * annotations properly import from @organon-methodology/testing and call testInvariant().
+ *
+ * This gate does NOT run tests — that's CI's job. It only checks structure:
+ * 1. Find files with @organon-invariant annotations
+ * 2. Verify they import from @organon-methodology/testing
+ * 3. Verify they contain testInvariant() calls
+ * 4. Report gaps
+ */
+import { joinPath } from './config.js';
+// ---------------------------------------------------------------------------
+// Constants
+// ---------------------------------------------------------------------------
+const DEFAULT_TEST_GLOBS = [
+    '**/*.test.ts',
+    '**/*.test.js',
+    '**/*.test.tsx',
+    '**/*.test.jsx',
+    '**/*.spec.ts',
+    '**/*.spec.js',
+];
+const ANNOTATION_RE = /@organon-invariant\s+INV-[\w-]+/;
+const TESTING_IMPORT_RE = /from\s+['"]@organon-methodology\/testing/;
+const TEST_INVARIANT_RE = /testInvariant\s*\(/;
+// ---------------------------------------------------------------------------
+// Public API
+// ---------------------------------------------------------------------------
+/**
+ * Verify that test files with @organon-invariant annotations
+ * properly use @organon-methodology/testing infrastructure.
+ */
+export async function verifyTier4Tests(options) {
+    const { projectRoot, config, fs } = options;
+    const testGlobs = config.testGlobs ?? DEFAULT_TEST_GLOBS;
+    const ignorePatterns = config.testIgnorePatterns ?? config.ignorePatterns;
+    const errors = [];
+    const warnings = [];
+    let filesScanned = 0;
+    let annotatedFiles = 0;
+    let validFiles = 0;
+    for (const pattern of testGlobs) {
+        const files = await fs.glob(pattern, { cwd: projectRoot, ignore: ignorePatterns });
+        for (const file of files) {
+            filesScanned++;
+            const absPath = joinPath(projectRoot, file);
+            let content;
+            try {
+                content = await fs.readFile(absPath);
+            }
+            catch {
+                continue;
+            }
+            // Only check files that have @organon-invariant annotations
+            if (!ANNOTATION_RE.test(content))
+                continue;
+            annotatedFiles++;
+            let isValid = true;
+            // Check for @organon-methodology/testing import
+            if (!TESTING_IMPORT_RE.test(content)) {
+                warnings.push({
+                    severity: 'warning',
+                    code: 'TIER4_MISSING_IMPORT',
+                    message: `Test file has @organon-invariant annotation but does not import from @organon-methodology/testing`,
+                    file,
+                    suggestion: `Add: import { testInvariant } from '@organon-methodology/testing/vitest';`,
+                });
+                isValid = false;
+            }
+            // Check for testInvariant() call
+            if (!TEST_INVARIANT_RE.test(content)) {
+                warnings.push({
+                    severity: 'warning',
+                    code: 'TIER4_MISSING_TEST_INVARIANT',
+                    message: `Test file has @organon-invariant annotation but does not call testInvariant()`,
+                    file,
+                    suggestion: `Wrap assertions with testInvariant('INV-ID', 'description', async () => { ... });`,
+                });
+                isValid = false;
+            }
+            if (isValid) {
+                validFiles++;
+            }
+        }
+    }
+    // Info warning when no annotated files found
+    if (annotatedFiles === 0 && filesScanned > 0) {
+        warnings.push({
+            severity: 'warning',
+            code: 'TIER4_NO_ANNOTATED_FILES',
+            message: `No test files found with @organon-invariant annotations (scanned ${filesScanned} file(s))`,
+            suggestion: `Add // @organon-invariant INV-ID comments to test files that verify invariants`,
+        });
+    }
+    return {
+        success: errors.length === 0,
+        filesScanned,
+        annotatedFiles,
+        validFiles,
+        errors,
+        warnings,
+    };
+}
+//# sourceMappingURL=verify-tier4-tests.js.map

package/dist/core/verify-tier4-tests.js.map

@@ -0,0 +1 @@
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package/dist/core/verify-tier4-tests.test.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=verify-tier4-tests.test.d.ts.map

package/dist/core/verify-tier4-tests.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"verify-tier4-tests.test.d.ts","sourceRoot":"","sources":["../../src/core/verify-tier4-tests.test.ts"],"names":[],"mappings":""}

package/dist/core/verify-tier4-tests.test.js

@@ -0,0 +1,140 @@
+import { describe, it, expect } from 'vitest';
+import { verifyTier4Tests } from './verify-tier4-tests.js';
+import { MemoryFileSystem } from './test-helpers.js';
+const PROJECT_ROOT = '/project';
+function makeConfig(overrides) {
+    return {
+        projectRoot: PROJECT_ROOT,
+        organonPaths: ['.'],
+        organonGlobs: ['**/ETHOS.md'],
+        ignorePatterns: ['node_modules/**'],
+        workflowPaths: {},
+        freshnessThresholdHours: 720,
+        testGlobs: ['**/*.test.ts'],
+        testIgnorePatterns: ['node_modules/**'],
+        ...overrides,
+    };
+}
+describe('verifyTier4Tests', () => {
+    it('passes when annotated files have proper imports and testInvariant calls', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/tests/my.test.ts': [
+                `// @organon-invariant INV-FOO-1`,
+                `import { testInvariant } from '@organon-methodology/testing/vitest';`,
+                `testInvariant('INV-FOO-1', 'test', async () => {});`,
+            ].join('\n'),
+        });
+        const result = await verifyTier4Tests({
+            projectRoot: PROJECT_ROOT,
+            config: makeConfig(),
+            fs,
+        });
+        expect(result.success).toBe(true);
+        expect(result.annotatedFiles).toBe(1);
+        expect(result.validFiles).toBe(1);
+        expect(result.warnings).toHaveLength(0);
+    });
+    it('warns when annotated file is missing @organon-methodology/testing import', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/tests/my.test.ts': [
+                `// @organon-invariant INV-FOO-1`,
+                `import { it } from 'vitest';`,
+                `it('test', () => {});`,
+            ].join('\n'),
+        });
+        const result = await verifyTier4Tests({
+            projectRoot: PROJECT_ROOT,
+            config: makeConfig(),
+            fs,
+        });
+        // Advisory gate — still passes
+        expect(result.success).toBe(true);
+        expect(result.warnings.some((w) => w.code === 'TIER4_MISSING_IMPORT')).toBe(true);
+        expect(result.warnings.some((w) => w.code === 'TIER4_MISSING_TEST_INVARIANT')).toBe(true);
+    });
+    it('warns when annotated file has import but no testInvariant call', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/tests/my.test.ts': [
+                `// @organon-invariant INV-FOO-1`,
+                `import { assertMaxValue } from '@organon-methodology/testing/vitest';`,
+                `// no testInvariant call`,
+            ].join('\n'),
+        });
+        const result = await verifyTier4Tests({
+            projectRoot: PROJECT_ROOT,
+            config: makeConfig(),
+            fs,
+        });
+        expect(result.success).toBe(true);
+        expect(result.warnings.some((w) => w.code === 'TIER4_MISSING_TEST_INVARIANT')).toBe(true);
+    });
+    it('ignores test files without annotations', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/tests/regular.test.ts': [
+                `import { it } from 'vitest';`,
+                `it('regular test', () => {});`,
+            ].join('\n'),
+        });
+        const result = await verifyTier4Tests({
+            projectRoot: PROJECT_ROOT,
+            config: makeConfig(),
+            fs,
+        });
+        expect(result.success).toBe(true);
+        expect(result.annotatedFiles).toBe(0);
+        expect(result.filesScanned).toBe(1);
+    });
+    it('warns when no annotated files found', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/tests/regular.test.ts': `// no annotations\nit('test', () => {});`,
+        });
+        const result = await verifyTier4Tests({
+            projectRoot: PROJECT_ROOT,
+            config: makeConfig(),
+            fs,
+        });
+        expect(result.success).toBe(true);
+        expect(result.warnings.some((w) => w.code === 'TIER4_NO_ANNOTATED_FILES')).toBe(true);
+    });
+    it('checks multiple files independently', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/tests/good.test.ts': [
+                `// @organon-invariant INV-FOO-1`,
+                `import { testInvariant } from '@organon-methodology/testing/vitest';`,
+                `testInvariant('INV-FOO-1', 'test', async () => {});`,
+            ].join('\n'),
+            '/project/tests/bad.test.ts': [
+                `// @organon-invariant INV-BAR-1`,
+                `import { it } from 'vitest';`,
+                `it('test', () => {});`,
+            ].join('\n'),
+        });
+        const result = await verifyTier4Tests({
+            projectRoot: PROJECT_ROOT,
+            config: makeConfig(),
+            fs,
+        });
+        expect(result.success).toBe(true); // Advisory
+        expect(result.annotatedFiles).toBe(2);
+        expect(result.validFiles).toBe(1);
+        expect(result.warnings.length).toBeGreaterThan(0);
+    });
+    it('reports warning suggestions with correct import path', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/tests/my.test.ts': [
+                `// @organon-invariant INV-FOO-1`,
+                `console.log('no imports at all');`,
+            ].join('\n'),
+        });
+        const result = await verifyTier4Tests({
+            projectRoot: PROJECT_ROOT,
+            config: makeConfig(),
+            fs,
+        });
+        const importWarning = result.warnings.find((w) => w.code === 'TIER4_MISSING_IMPORT');
+        expect(importWarning).toBeDefined();
+        expect(importWarning.suggestion).toContain('@organon-methodology/testing/vitest');
+        expect(importWarning.file).toBe('tests/my.test.ts');
+    });
+});
+//# sourceMappingURL=verify-tier4-tests.test.js.map

package/dist/core/verify-tier4-tests.test.js.map

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package/dist/core/verify-triplets.d.ts

@@ -0,0 +1,17 @@
+/**
+ * Protocol ↔ Workflow ↔ Tool binding verification.
+ *
+ * Checks that the three-layer architecture is properly connected:
+ * - Every automated protocol has a workflow binding
+ * - Every workflow references back to its protocol
+ * - No orphaned workflows (workflow without a protocol)
+ * - No phantom automation (protocol claims automated but workflow is missing)
+ */
+import type { FileSystem, OrganonConfig, VerifyTripletsResult } from './types.js';
+export interface VerifyTripletsOptions {
+    projectRoot: string;
+    config: OrganonConfig;
+    fs: FileSystem;
+}
+export declare function verifyTriplets(options: VerifyTripletsOptions): Promise<VerifyTripletsResult>;
+//# sourceMappingURL=verify-triplets.d.ts.map

package/dist/core/verify-triplets.d.ts.map

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