@organon-methodology/tools 0.3.0 → 0.4.1

package/dist/core/verify-references.js

@@ -0,0 +1,157 @@
+/**
+ * References verification gate (blocking).
+ *
+ * Checks that cross-file references actually resolve:
+ * - inherits_from names → real organon file name fields
+ * - related_domains / related_features → real organon names
+ * - Workflow loads: paths → exist on disk
+ * - Workflow protocol_file paths → exist on disk
+ *
+ * @organon-invariant INV-TOOLS-2 every-command-has-tests
+ */
+import { parseFrontmatter } from './frontmatter-parser.js';
+import { joinPath } from './config.js';
+import { discoverOrganonFiles } from './discover.js';
+// ---------------------------------------------------------------------------
+// Main
+// ---------------------------------------------------------------------------
+export async function verifyReferences(options) {
+    const { projectRoot, config, fs } = options;
+    const errors = [];
+    const warnings = [];
+    // 1. Collect all organon files + their frontmatter
+    const organonFiles = await discoverOrganonFiles(projectRoot, config, fs);
+    const allFrontmatter = new Map();
+    for (const file of organonFiles) {
+        const absPath = joinPath(projectRoot, file);
+        try {
+            const content = await fs.readFile(absPath);
+            const { frontmatter } = parseFrontmatter(content);
+            allFrontmatter.set(file, frontmatter);
+        }
+        catch {
+            allFrontmatter.set(file, null);
+        }
+    }
+    // Build a set of known organon names for quick lookup
+    const knownNames = new Set();
+    for (const [, fm] of allFrontmatter) {
+        if (fm?.name)
+            knownNames.add(fm.name);
+    }
+    // 2. Check organon file references
+    for (const [file, fm] of allFrontmatter) {
+        if (!fm)
+            continue;
+        // inherits_from → must resolve to a real organon name
+        if (fm.inherits_from) {
+            for (const parent of fm.inherits_from) {
+                if (!knownNames.has(parent)) {
+                    errors.push({
+                        severity: 'error',
+                        code: 'REFERENCE_BROKEN_INHERIT',
+                        message: `inherits_from references '${parent}' but no organon with that name found`,
+                        file,
+                    });
+                }
+            }
+        }
+        // related_domains → must resolve
+        if (fm.related_domains) {
+            for (const domain of fm.related_domains) {
+                if (!knownNames.has(domain)) {
+                    errors.push({
+                        severity: 'error',
+                        code: 'REFERENCE_BROKEN_DOMAIN',
+                        message: `related_domains references '${domain}' but no organon with that name found`,
+                        file,
+                    });
+                }
+            }
+        }
+        // related_features → must resolve
+        if (fm.related_features) {
+            for (const feature of fm.related_features) {
+                if (!knownNames.has(feature)) {
+                    errors.push({
+                        severity: 'error',
+                        code: 'REFERENCE_BROKEN_FEATURE',
+                        message: `related_features references '${feature}' but no organon with that name found`,
+                        file,
+                    });
+                }
+            }
+        }
+    }
+    // 3. Check workflow file references
+    const workflowFiles = await discoverWorkflowFiles(projectRoot, config, fs);
+    for (const file of workflowFiles) {
+        const absPath = joinPath(projectRoot, file);
+        let content;
+        try {
+            content = await fs.readFile(absPath);
+        }
+        catch {
+            continue;
+        }
+        const { frontmatter } = parseFrontmatter(content);
+        if (!frontmatter)
+            continue;
+        // loads: paths → must exist on disk
+        const loads = frontmatter['loads'];
+        if (loads && Array.isArray(loads)) {
+            for (const loadPath of loads) {
+                const absLoadPath = joinPath(projectRoot, loadPath);
+                if (!await fs.exists(absLoadPath)) {
+                    errors.push({
+                        severity: 'error',
+                        code: 'REFERENCE_BROKEN_LOADS',
+                        message: `Workflow loads path '${loadPath}' does not exist on disk`,
+                        file,
+                    });
+                }
+            }
+        }
+        // protocol_file → must exist on disk
+        const protocolFile = frontmatter['protocol_file'];
+        if (protocolFile) {
+            const absProtoPath = joinPath(projectRoot, protocolFile);
+            if (!await fs.exists(absProtoPath)) {
+                errors.push({
+                    severity: 'error',
+                    code: 'REFERENCE_BROKEN_PROTOCOL_FILE',
+                    message: `Workflow protocol_file '${protocolFile}' does not exist on disk`,
+                    file,
+                });
+            }
+        }
+    }
+    return {
+        success: errors.length === 0,
+        errors,
+        warnings,
+    };
+}
+// ---------------------------------------------------------------------------
+// Helpers
+// ---------------------------------------------------------------------------
+async function discoverWorkflowFiles(projectRoot, config, fs) {
+    const files = new Set();
+    const paths = config.workflowPaths;
+    const searchPaths = [
+        paths.claudeCode,
+        paths.cursor,
+        paths.generic,
+    ].filter((p) => p !== undefined);
+    for (const dir of searchPaths) {
+        const fullDir = joinPath(projectRoot, dir);
+        if (await fs.exists(fullDir)) {
+            const matches = await fs.glob('**/*.md', { cwd: fullDir, ignore: [] });
+            for (const m of matches) {
+                files.add(joinPath(dir, m));
+            }
+        }
+    }
+    return [...files].sort();
+}
+//# sourceMappingURL=verify-references.js.map

package/dist/core/verify-references.js.map

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package/dist/core/verify-references.test.d.ts

@@ -0,0 +1,7 @@
+/**
+ * Tests for references verification gate.
+ *
+ * @organon-invariant INV-TOOLS-2 every-command-has-tests
+ */
+export {};
+//# sourceMappingURL=verify-references.test.d.ts.map

package/dist/core/verify-references.test.d.ts.map

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

package/dist/core/verify-references.test.js

@@ -0,0 +1,88 @@
+/**
+ * Tests for references verification gate.
+ *
+ * @organon-invariant INV-TOOLS-2 every-command-has-tests
+ */
+import { describe, it, expect } from 'vitest';
+import { verifyReferences } from './verify-references.js';
+import { MemoryFileSystem, makeEthos, makeWorkflow } from './test-helpers.js';
+function makeConfig(projectRoot, extraPaths = []) {
+    return {
+        projectRoot,
+        organonPaths: ['.', ...extraPaths],
+        organonGlobs: ['**/ETHOS.md', '**/PHILOSOPHY.md', '**/README.md'],
+        ignorePatterns: [],
+        workflowPaths: { generic: 'workflows' },
+        freshnessThresholdHours: 24,
+    };
+}
+describe('verifyReferences', () => {
+    it('passes when all references resolve', async () => {
+        const parentEthos = makeEthos({ name: 'parent', scope: 'product' });
+        const childEthos = makeEthos({ name: 'child', scope: 'domain', extra: { inherits_from: '["parent"]' } });
+        const fs = new MemoryFileSystem({
+            '/project/ETHOS.md': parentEthos,
+            '/project/domains/child/ETHOS.md': childEthos,
+        });
+        const config = makeConfig('/project', ['domains']);
+        const result = await verifyReferences({ projectRoot: '/project', config, fs });
+        expect(result.success).toBe(true);
+    });
+    it('reports broken inherits_from reference', async () => {
+        const ethos = makeEthos({ name: 'child', scope: 'domain', extra: { inherits_from: '["nonexistent-parent"]' } });
+        const fs = new MemoryFileSystem({
+            '/project/ETHOS.md': ethos,
+        });
+        const config = makeConfig('/project');
+        const result = await verifyReferences({ projectRoot: '/project', config, fs });
+        expect(result.success).toBe(false);
+        expect(result.errors).toContainEqual(expect.objectContaining({ code: 'REFERENCE_BROKEN_INHERIT' }));
+    });
+    it('reports broken related_domains reference', async () => {
+        const ethos = makeEthos({ name: 'test', scope: 'domain', extra: { related_domains: '["ghost-domain"]' } });
+        const fs = new MemoryFileSystem({
+            '/project/ETHOS.md': ethos,
+        });
+        const config = makeConfig('/project');
+        const result = await verifyReferences({ projectRoot: '/project', config, fs });
+        expect(result.success).toBe(false);
+        expect(result.errors).toContainEqual(expect.objectContaining({ code: 'REFERENCE_BROKEN_DOMAIN' }));
+    });
+    it('reports broken related_features reference', async () => {
+        const ethos = makeEthos({ name: 'test', scope: 'domain', extra: { related_features: '["ghost-feature"]' } });
+        const fs = new MemoryFileSystem({
+            '/project/ETHOS.md': ethos,
+        });
+        const config = makeConfig('/project');
+        const result = await verifyReferences({ projectRoot: '/project', config, fs });
+        expect(result.success).toBe(false);
+        expect(result.errors).toContainEqual(expect.objectContaining({ code: 'REFERENCE_BROKEN_FEATURE' }));
+    });
+    it('reports broken workflow loads path', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/workflows/test.md': makeWorkflow({ loads: ['/nonexistent.md'] }),
+        });
+        const config = makeConfig('/project');
+        const result = await verifyReferences({ projectRoot: '/project', config, fs });
+        expect(result.success).toBe(false);
+        expect(result.errors).toContainEqual(expect.objectContaining({ code: 'REFERENCE_BROKEN_LOADS' }));
+    });
+    it('reports broken workflow protocol_file path', async () => {
+        const workflow = makeWorkflow({ protocolFile: 'nonexistent/PROTOCOLS.md' });
+        const fs = new MemoryFileSystem({
+            '/project/workflows/test.md': workflow,
+            '/project/ETHOS.md': '# ethos',
+        });
+        const config = makeConfig('/project');
+        const result = await verifyReferences({ projectRoot: '/project', config, fs });
+        expect(result.success).toBe(false);
+        expect(result.errors).toContainEqual(expect.objectContaining({ code: 'REFERENCE_BROKEN_PROTOCOL_FILE' }));
+    });
+    it('passes when no organon files or workflows exist', async () => {
+        const fs = new MemoryFileSystem({});
+        const config = makeConfig('/project');
+        const result = await verifyReferences({ projectRoot: '/project', config, fs });
+        expect(result.success).toBe(true);
+    });
+});
+//# sourceMappingURL=verify-references.test.js.map

package/dist/core/verify-references.test.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"verify-references.test.js","sourceRoot":"","sources":["../../src/core/verify-references.test.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,QAAQ,EAAE,EAAE,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAC;AAC9C,OAAO,EAAE,gBAAgB,EAAE,MAAM,wBAAwB,CAAC;AAC1D,OAAO,EAAE,gBAAgB,EAAE,SAAS,EAAE,YAAY,EAAE,MAAM,mBAAmB,CAAC;AAG9E,SAAS,UAAU,CAAC,WAAmB,EAAE,aAAuB,EAAE;IAChE,OAAO;QACL,WAAW;QACX,YAAY,EAAE,CAAC,GAAG,EAAE,GAAG,UAAU,CAAC;QAClC,YAAY,EAAE,CAAC,aAAa,EAAE,kBAAkB,EAAE,cAAc,CAAC;QACjE,cAAc,EAAE,EAAE;QAClB,aAAa,EAAE,EAAE,OAAO,EAAE,WAAW,EAAE;QACvC,uBAAuB,EAAE,EAAE;KAC5B,CAAC;AACJ,CAAC;AAED,QAAQ,CAAC,kBAAkB,EAAE,GAAG,EAAE;IAChC,EAAE,CAAC,oCAAoC,EAAE,KAAK,IAAI,EAAE;QAClD,MAAM,WAAW,GAAG,SAAS,CAAC,EAAE,IAAI,EAAE,QAAQ,EAAE,KAAK,EAAE,SAAS,EAAE,CAAC,CAAC;QACpE,MAAM,UAAU,GAAG,SAAS,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,QAAQ,EAAE,KAAK,EAAE,EAAE,aAAa,EAAE,YAAY,EAAE,EAAE,CAAC,CAAC;QACzG,MAAM,EAAE,GAAG,IAAI,gBAAgB,CAAC;YAC9B,mBAAmB,EAAE,WAAW;YAChC,iCAAiC,EAAE,UAAU;SAC9C,CAAC,CAAC;QACH,MAAM,MAAM,GAAG,UAAU,CAAC,UAAU,EAAE,CAAC,SAAS,CAAC,CAAC,CAAC;QACnD,MAAM,MAAM,GAAG,MAAM,gBAAgB,CAAC,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,CAAC;QAC/E,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IACpC,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,wCAAwC,EAAE,KAAK,IAAI,EAAE;QACtD,MAAM,KAAK,GAAG,SAAS,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,QAAQ,EAAE,KAAK,EAAE,EAAE,aAAa,EAAE,wBAAwB,EAAE,EAAE,CAAC,CAAC;QAChH,MAAM,EAAE,GAAG,IAAI,gBAAgB,CAAC;YAC9B,mBAAmB,EAAE,KAAK;SAC3B,CAAC,CAAC;QACH,MAAM,MAAM,GAAG,UAAU,CAAC,UAAU,CAAC,CAAC;QACtC,MAAM,MAAM,GAAG,MAAM,gBAAgB,CAAC,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,CAAC;QAC/E,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;QACnC,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,cAAc,CAClC,MAAM,CAAC,gBAAgB,CAAC,EAAE,IAAI,EAAE,0BAA0B,EAAE,CAAC,CAC9D,CAAC;IACJ,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,0CAA0C,EAAE,KAAK,IAAI,EAAE;QACxD,MAAM,KAAK,GAAG,SAAS,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,QAAQ,EAAE,KAAK,EAAE,EAAE,eAAe,EAAE,kBAAkB,EAAE,EAAE,CAAC,CAAC;QAC3G,MAAM,EAAE,GAAG,IAAI,gBAAgB,CAAC;YAC9B,mBAAmB,EAAE,KAAK;SAC3B,CAAC,CAAC;QACH,MAAM,MAAM,GAAG,UAAU,CAAC,UAAU,CAAC,CAAC;QACtC,MAAM,MAAM,GAAG,MAAM,gBAAgB,CAAC,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,CAAC;QAC/E,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;QACnC,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,cAAc,CAClC,MAAM,CAAC,gBAAgB,CAAC,EAAE,IAAI,EAAE,yBAAyB,EAAE,CAAC,CAC7D,CAAC;IACJ,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,2CAA2C,EAAE,KAAK,IAAI,EAAE;QACzD,MAAM,KAAK,GAAG,SAAS,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,QAAQ,EAAE,KAAK,EAAE,EAAE,gBAAgB,EAAE,mBAAmB,EAAE,EAAE,CAAC,CAAC;QAC7G,MAAM,EAAE,GAAG,IAAI,gBAAgB,CAAC;YAC9B,mBAAmB,EAAE,KAAK;SAC3B,CAAC,CAAC;QACH,MAAM,MAAM,GAAG,UAAU,CAAC,UAAU,CAAC,CAAC;QACtC,MAAM,MAAM,GAAG,MAAM,gBAAgB,CAAC,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,CAAC;QAC/E,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;QACnC,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,cAAc,CAClC,MAAM,CAAC,gBAAgB,CAAC,EAAE,IAAI,EAAE,0BAA0B,EAAE,CAAC,CAC9D,CAAC;IACJ,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,oCAAoC,EAAE,KAAK,IAAI,EAAE;QAClD,MAAM,EAAE,GAAG,IAAI,gBAAgB,CAAC;YAC9B,4BAA4B,EAAE,YAAY,CAAC,EAAE,KAAK,EAAE,CAAC,iBAAiB,CAAC,EAAE,CAAC;SAC3E,CAAC,CAAC;QACH,MAAM,MAAM,GAAG,UAAU,CAAC,UAAU,CAAC,CAAC;QACtC,MAAM,MAAM,GAAG,MAAM,gBAAgB,CAAC,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,CAAC;QAC/E,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;QACnC,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,cAAc,CAClC,MAAM,CAAC,gBAAgB,CAAC,EAAE,IAAI,EAAE,wBAAwB,EAAE,CAAC,CAC5D,CAAC;IACJ,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,4CAA4C,EAAE,KAAK,IAAI,EAAE;QAC1D,MAAM,QAAQ,GAAG,YAAY,CAAC,EAAE,YAAY,EAAE,0BAA0B,EAAE,CAAC,CAAC;QAC5E,MAAM,EAAE,GAAG,IAAI,gBAAgB,CAAC;YAC9B,4BAA4B,EAAE,QAAQ;YACtC,mBAAmB,EAAE,SAAS;SAC/B,CAAC,CAAC;QACH,MAAM,MAAM,GAAG,UAAU,CAAC,UAAU,CAAC,CAAC;QACtC,MAAM,MAAM,GAAG,MAAM,gBAAgB,CAAC,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,CAAC;QAC/E,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;QACnC,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,cAAc,CAClC,MAAM,CAAC,gBAAgB,CAAC,EAAE,IAAI,EAAE,gCAAgC,EAAE,CAAC,CACpE,CAAC;IACJ,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,iDAAiD,EAAE,KAAK,IAAI,EAAE;QAC/D,MAAM,EAAE,GAAG,IAAI,gBAAgB,CAAC,EAAE,CAAC,CAAC;QACpC,MAAM,MAAM,GAAG,UAAU,CAAC,UAAU,CAAC,CAAC;QACtC,MAAM,MAAM,GAAG,MAAM,gBAAgB,CAAC,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,CAAC;QAC/E,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IACpC,CAAC,CAAC,CAAC;AACL,CAAC,CAAC,CAAC"}

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

@@ -1 +1 @@
-{"version":3,"file":"verify-triplets.d.ts","sourceRoot":"","sources":["../../src/core/verify-triplets.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAIH,OAAO,KAAK,EAGV,UAAU,EAEV,aAAa,EAGb,oBAAoB,EACrB,MAAM,YAAY,CAAC;AAMpB,MAAM,WAAW,qBAAqB;IACpC,WAAW,EAAE,MAAM,CAAC;IACpB,MAAM,EAAE,aAAa,CAAC;IACtB,EAAE,EAAE,UAAU,CAAC;CAChB;AAMD,wBAAsB,cAAc,CAClC,OAAO,EAAE,qBAAqB,GAC7B,OAAO,CAAC,oBAAoB,CAAC,CA6J/B"}
+{"version":3,"file":"verify-triplets.d.ts","sourceRoot":"","sources":["../../src/core/verify-triplets.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAKH,OAAO,KAAK,EAGV,UAAU,EAEV,aAAa,EAGb,oBAAoB,EACrB,MAAM,YAAY,CAAC;AAMpB,MAAM,WAAW,qBAAqB;IACpC,WAAW,EAAE,MAAM,CAAC;IACpB,MAAM,EAAE,aAAa,CAAC;IACtB,EAAE,EAAE,UAAU,CAAC;CAChB;AAMD,wBAAsB,cAAc,CAClC,OAAO,EAAE,qBAAqB,GAC7B,OAAO,CAAC,oBAAoB,CAAC,CA6J/B"}

package/dist/core/verify-triplets.js

@@ -9,6 +9,7 @@
  */
 import { parseFrontmatter } from './frontmatter-parser.js';
 import { joinPath } from './config.js';
+import { discoverOrganonFiles } from './discover.js';
 // ---------------------------------------------------------------------------
 // Main
 // ---------------------------------------------------------------------------
@@ -198,20 +199,4 @@ async function discoverWorkflowFiles(projectRoot, config, fs) {
     }
     return [...files].sort();
 }
-async function discoverOrganonFiles(projectRoot, config, fs) {
-    const allFiles = new Set();
-    for (const organonPath of config.organonPaths) {
-        for (const pattern of config.organonGlobs) {
-            const fullPattern = organonPath === '.' ? pattern : `${organonPath}/${pattern}`;
-            const matches = await fs.glob(fullPattern, {
-                cwd: projectRoot,
-                ignore: config.ignorePatterns,
-            });
-            for (const m of matches) {
-                allFiles.add(m);
-            }
-        }
-    }
-    return [...allFiles].sort();
-}
 //# sourceMappingURL=verify-triplets.js.map

package/dist/core/verify-triplets.js.map

@@ -1 +1 @@
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package/dist/core/verify-version-alignment.d.ts

@@ -0,0 +1,20 @@
+/**
+ * Version alignment gate (advisory).
+ *
+ * Checks:
+ * 1. organon.config.json methodology_version matches bundled METHODOLOGY_VERSION
+ *
+ * @organon-invariant INV-TOOLS-2 every-command-has-tests
+ */
+import type { DiagnosticMessage, FileSystem, OrganonConfig } from './types.js';
+export interface VersionAlignmentResult {
+    success: boolean;
+    errors: DiagnosticMessage[];
+    warnings: DiagnosticMessage[];
+}
+export declare function verifyVersionAlignment(options: {
+    projectRoot: string;
+    config: OrganonConfig;
+    fs: FileSystem;
+}): Promise<VersionAlignmentResult>;
+//# sourceMappingURL=verify-version-alignment.d.ts.map

package/dist/core/verify-version-alignment.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"verify-version-alignment.d.ts","sourceRoot":"","sources":["../../src/core/verify-version-alignment.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAIH,OAAO,KAAK,EACV,iBAAiB,EACjB,UAAU,EACV,aAAa,EACd,MAAM,YAAY,CAAC;AAMpB,MAAM,WAAW,sBAAsB;IACrC,OAAO,EAAE,OAAO,CAAC;IACjB,MAAM,EAAE,iBAAiB,EAAE,CAAC;IAC5B,QAAQ,EAAE,iBAAiB,EAAE,CAAC;CAC/B;AAMD,wBAAsB,sBAAsB,CAAC,OAAO,EAAE;IACpD,WAAW,EAAE,MAAM,CAAC;IACpB,MAAM,EAAE,aAAa,CAAC;IACtB,EAAE,EAAE,UAAU,CAAC;CAChB,GAAG,OAAO,CAAC,sBAAsB,CAAC,CA8BlC"}

package/dist/core/verify-version-alignment.js

@@ -0,0 +1,43 @@
+/**
+ * Version alignment gate (advisory).
+ *
+ * Checks:
+ * 1. organon.config.json methodology_version matches bundled METHODOLOGY_VERSION
+ *
+ * @organon-invariant INV-TOOLS-2 every-command-has-tests
+ */
+import { joinPath } from './config.js';
+import { METHODOLOGY_VERSION } from '../templates/config.js';
+// ---------------------------------------------------------------------------
+// Main
+// ---------------------------------------------------------------------------
+export async function verifyVersionAlignment(options) {
+    const { projectRoot, fs } = options;
+    const errors = [];
+    const warnings = [];
+    // 1. Check organon.config.json methodology_version vs bundled
+    try {
+        const configPath = joinPath(projectRoot, 'organon.config.json');
+        const configContent = await fs.readFile(configPath);
+        const config = JSON.parse(configContent);
+        const configVersion = config.methodology_version;
+        if (configVersion && configVersion !== METHODOLOGY_VERSION) {
+            warnings.push({
+                severity: 'warning',
+                code: 'VERSION_METHODOLOGY_DRIFT',
+                message: `organon.config.json methodology_version '${configVersion}' does not match CLI version '${METHODOLOGY_VERSION}'`,
+                file: 'organon.config.json',
+                suggestion: `Run 'organon upgrade' or update methodology_version to '${METHODOLOGY_VERSION}'`,
+            });
+        }
+    }
+    catch {
+        // No config file — not an error for this gate
+    }
+    return {
+        success: true, // Advisory gate — always passes
+        errors,
+        warnings,
+    };
+}
+//# sourceMappingURL=verify-version-alignment.js.map

package/dist/core/verify-version-alignment.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"verify-version-alignment.js","sourceRoot":"","sources":["../../src/core/verify-version-alignment.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAE,QAAQ,EAAE,MAAM,aAAa,CAAC;AACvC,OAAO,EAAE,mBAAmB,EAAE,MAAM,wBAAwB,CAAC;AAiB7D,8EAA8E;AAC9E,OAAO;AACP,8EAA8E;AAE9E,MAAM,CAAC,KAAK,UAAU,sBAAsB,CAAC,OAI5C;IACC,MAAM,EAAE,WAAW,EAAE,EAAE,EAAE,GAAG,OAAO,CAAC;IACpC,MAAM,MAAM,GAAwB,EAAE,CAAC;IACvC,MAAM,QAAQ,GAAwB,EAAE,CAAC;IAEzC,8DAA8D;IAC9D,IAAI,CAAC;QACH,MAAM,UAAU,GAAG,QAAQ,CAAC,WAAW,EAAE,qBAAqB,CAAC,CAAC;QAChE,MAAM,aAAa,GAAG,MAAM,EAAE,CAAC,QAAQ,CAAC,UAAU,CAAC,CAAC;QACpD,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,aAAa,CAAC,CAAC;QACzC,MAAM,aAAa,GAAG,MAAM,CAAC,mBAAmB,CAAC;QAEjD,IAAI,aAAa,IAAI,aAAa,KAAK,mBAAmB,EAAE,CAAC;YAC3D,QAAQ,CAAC,IAAI,CAAC;gBACZ,QAAQ,EAAE,SAAS;gBACnB,IAAI,EAAE,2BAA2B;gBACjC,OAAO,EAAE,4CAA4C,aAAa,iCAAiC,mBAAmB,GAAG;gBACzH,IAAI,EAAE,qBAAqB;gBAC3B,UAAU,EAAE,2DAA2D,mBAAmB,GAAG;aAC9F,CAAC,CAAC;QACL,CAAC;IACH,CAAC;IAAC,MAAM,CAAC;QACP,8CAA8C;IAChD,CAAC;IAED,OAAO;QACL,OAAO,EAAE,IAAI,EAAE,gCAAgC;QAC/C,MAAM;QACN,QAAQ;KACT,CAAC;AACJ,CAAC"}

package/dist/core/verify-version-alignment.test.d.ts

@@ -0,0 +1,7 @@
+/**
+ * Tests for version alignment gate.
+ *
+ * @organon-invariant INV-TOOLS-2 every-command-has-tests
+ */
+export {};
+//# sourceMappingURL=verify-version-alignment.test.d.ts.map

package/dist/core/verify-version-alignment.test.d.ts.map

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

package/dist/core/verify-version-alignment.test.js

@@ -0,0 +1,57 @@
+/**
+ * Tests for version alignment gate.
+ *
+ * @organon-invariant INV-TOOLS-2 every-command-has-tests
+ */
+import { describe, it, expect } from 'vitest';
+import { verifyVersionAlignment } from './verify-version-alignment.js';
+import { MemoryFileSystem } from './test-helpers.js';
+import { METHODOLOGY_VERSION } from '../templates/config.js';
+function makeConfig(projectRoot) {
+    return {
+        projectRoot,
+        organonPaths: ['.'],
+        organonGlobs: ['**/ETHOS.md'],
+        ignorePatterns: [],
+        workflowPaths: {},
+        freshnessThresholdHours: 24,
+    };
+}
+describe('verifyVersionAlignment', () => {
+    it('passes when methodology_version matches CLI', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/organon.config.json': JSON.stringify({ methodology_version: METHODOLOGY_VERSION }),
+        });
+        const config = makeConfig('/project');
+        const result = await verifyVersionAlignment({ projectRoot: '/project', config, fs });
+        expect(result.success).toBe(true);
+        expect(result.warnings).toHaveLength(0);
+    });
+    it('warns when methodology_version drifts from CLI', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/organon.config.json': JSON.stringify({ methodology_version: '0.1.0' }),
+        });
+        const config = makeConfig('/project');
+        const result = await verifyVersionAlignment({ projectRoot: '/project', config, fs });
+        expect(result.success).toBe(true); // Advisory
+        expect(result.warnings).toContainEqual(expect.objectContaining({ code: 'VERSION_METHODOLOGY_DRIFT' }));
+    });
+    it('passes when no config file exists', async () => {
+        const fs = new MemoryFileSystem({});
+        const config = makeConfig('/project');
+        const result = await verifyVersionAlignment({ projectRoot: '/project', config, fs });
+        expect(result.success).toBe(true);
+        expect(result.warnings).toHaveLength(0);
+    });
+    it('does not check cross-package version alignment', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/organon.config.json': JSON.stringify({ methodology_version: METHODOLOGY_VERSION }),
+            '/project/packages/tools/package.json': JSON.stringify({ version: '1.0.0' }),
+            '/project/packages/testing/package.json': JSON.stringify({ version: '0.9.0' }),
+        });
+        const config = makeConfig('/project');
+        const result = await verifyVersionAlignment({ projectRoot: '/project', config, fs });
+        expect(result.warnings).toHaveLength(0);
+    });
+});
+//# sourceMappingURL=verify-version-alignment.test.js.map

package/dist/core/verify-version-alignment.test.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"verify-version-alignment.test.js","sourceRoot":"","sources":["../../src/core/verify-version-alignment.test.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,QAAQ,EAAE,EAAE,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAC;AAC9C,OAAO,EAAE,sBAAsB,EAAE,MAAM,+BAA+B,CAAC;AACvE,OAAO,EAAE,gBAAgB,EAAE,MAAM,mBAAmB,CAAC;AACrD,OAAO,EAAE,mBAAmB,EAAE,MAAM,wBAAwB,CAAC;AAG7D,SAAS,UAAU,CAAC,WAAmB;IACrC,OAAO;QACL,WAAW;QACX,YAAY,EAAE,CAAC,GAAG,CAAC;QACnB,YAAY,EAAE,CAAC,aAAa,CAAC;QAC7B,cAAc,EAAE,EAAE;QAClB,aAAa,EAAE,EAAE;QACjB,uBAAuB,EAAE,EAAE;KAC5B,CAAC;AACJ,CAAC;AAED,QAAQ,CAAC,wBAAwB,EAAE,GAAG,EAAE;IACtC,EAAE,CAAC,6CAA6C,EAAE,KAAK,IAAI,EAAE;QAC3D,MAAM,EAAE,GAAG,IAAI,gBAAgB,CAAC;YAC9B,8BAA8B,EAAE,IAAI,CAAC,SAAS,CAAC,EAAE,mBAAmB,EAAE,mBAAmB,EAAE,CAAC;SAC7F,CAAC,CAAC;QACH,MAAM,MAAM,GAAG,UAAU,CAAC,UAAU,CAAC,CAAC;QACtC,MAAM,MAAM,GAAG,MAAM,sBAAsB,CAAC,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,CAAC;QACrF,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QAClC,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC;IAC1C,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,gDAAgD,EAAE,KAAK,IAAI,EAAE;QAC9D,MAAM,EAAE,GAAG,IAAI,gBAAgB,CAAC;YAC9B,8BAA8B,EAAE,IAAI,CAAC,SAAS,CAAC,EAAE,mBAAmB,EAAE,OAAO,EAAE,CAAC;SACjF,CAAC,CAAC;QACH,MAAM,MAAM,GAAG,UAAU,CAAC,UAAU,CAAC,CAAC;QACtC,MAAM,MAAM,GAAG,MAAM,sBAAsB,CAAC,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,CAAC;QACrF,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,WAAW;QAC9C,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,cAAc,CACpC,MAAM,CAAC,gBAAgB,CAAC,EAAE,IAAI,EAAE,2BAA2B,EAAE,CAAC,CAC/D,CAAC;IACJ,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,mCAAmC,EAAE,KAAK,IAAI,EAAE;QACjD,MAAM,EAAE,GAAG,IAAI,gBAAgB,CAAC,EAAE,CAAC,CAAC;QACpC,MAAM,MAAM,GAAG,UAAU,CAAC,UAAU,CAAC,CAAC;QACtC,MAAM,MAAM,GAAG,MAAM,sBAAsB,CAAC,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,CAAC;QACrF,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QAClC,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC;IAC1C,CAAC,CAAC,CAAC;IAEH,EAAE,CAAC,gDAAgD,EAAE,KAAK,IAAI,EAAE;QAC9D,MAAM,EAAE,GAAG,IAAI,gBAAgB,CAAC;YAC9B,8BAA8B,EAAE,IAAI,CAAC,SAAS,CAAC,EAAE,mBAAmB,EAAE,mBAAmB,EAAE,CAAC;YAC5F,sCAAsC,EAAE,IAAI,CAAC,SAAS,CAAC,EAAE,OAAO,EAAE,OAAO,EAAE,CAAC;YAC5E,wCAAwC,EAAE,IAAI,CAAC,SAAS,CAAC,EAAE,OAAO,EAAE,OAAO,EAAE,CAAC;SAC/E,CAAC,CAAC;QACH,MAAM,MAAM,GAAG,UAAU,CAAC,UAAU,CAAC,CAAC;QACtC,MAAM,MAAM,GAAG,MAAM,sBAAsB,CAAC,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,CAAC;QACrF,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC;IAC1C,CAAC,CAAC,CAAC;AACL,CAAC,CAAC,CAAC"}

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

@@ -1 +1 @@
-{"version":3,"file":"verify.d.ts","sourceRoot":"","sources":["../../src/core/verify.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAQH,OAAO,KAAK,EAEV,UAAU,EACV,aAAa,EACb,YAAY,EAEZ,YAAY,EACb,MAAM,YAAY,CAAC;AAMpB,MAAM,WAAW,aAAa;IAC5B,WAAW,EAAE,MAAM,CAAC;IACpB,MAAM,EAAE,aAAa,CAAC;IACtB,EAAE,EAAE,UAAU,CAAC;IACf,2EAA2E;IAC3E,KAAK,CAAC,EAAE,MAAM,EAAE,CAAC;CAClB;AAQD,wBAAgB,YAAY,CAAC,IAAI,EAAE,MAAM,EAAE,EAAE,EAAE,YAAY,GAAG,IAAI,CAEjE;AAED,wBAAgB,kBAAkB,IAAI,MAAM,EAAE,CAE7C;AAkGD,wBAAsB,MAAM,CAAC,OAAO,EAAE,aAAa,GAAG,OAAO,CAAC,YAAY,CAAC,CAwD1E"}
+{"version":3,"file":"verify.d.ts","sourceRoot":"","sources":["../../src/core/verify.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAWH,OAAO,KAAK,EAEV,UAAU,EACV,aAAa,EACb,YAAY,EAEZ,YAAY,EACb,MAAM,YAAY,CAAC;AAMpB,MAAM,WAAW,aAAa;IAC5B,WAAW,EAAE,MAAM,CAAC;IACpB,MAAM,EAAE,aAAa,CAAC;IACtB,EAAE,EAAE,UAAU,CAAC;IACf,2EAA2E;IAC3E,KAAK,CAAC,EAAE,MAAM,EAAE,CAAC;CAClB;AAQD,wBAAgB,YAAY,CAAC,IAAI,EAAE,MAAM,EAAE,EAAE,EAAE,YAAY,GAAG,IAAI,CAEjE;AAED,wBAAgB,kBAAkB,IAAI,MAAM,EAAE,CAE7C;AAmID,wBAAsB,MAAM,CAAC,OAAO,EAAE,aAAa,GAAG,OAAO,CAAC,YAAY,CAAC,CAwD1E"}

package/dist/core/verify.js

@@ -11,6 +11,9 @@ import { health as runHealth } from './health.js';
 import { computeInvariantCoverage } from './invariant-coverage.js';
 import { validateWorkflow } from './validate-workflow.js';
 import { verifyTier4Tests } from './verify-tier4-tests.js';
+import { verifyPlaceholders } from './verify-placeholders.js';
+import { verifyReferences } from './verify-references.js';
+import { verifyVersionAlignment } from './verify-version-alignment.js';
 // ---------------------------------------------------------------------------
 // Gate registry
 // ---------------------------------------------------------------------------
@@ -95,6 +98,33 @@ const tier4TestsGate = async ({ projectRoot, config, fs }) => {
         warnings: result.warnings,
     };
 };
+const placeholderDetectionGate = async ({ projectRoot, config, fs }) => {
+    const result = await verifyPlaceholders({ projectRoot, config, fs });
+    return {
+        gate: 'placeholder-detection',
+        passed: true, // Advisory — always passes
+        errors: result.errors,
+        warnings: result.warnings,
+    };
+};
+const referencesGate = async ({ projectRoot, config, fs }) => {
+    const result = await verifyReferences({ projectRoot, config, fs });
+    return {
+        gate: 'references',
+        passed: result.success,
+        errors: result.errors,
+        warnings: result.warnings,
+    };
+};
+const versionAlignmentGate = async ({ projectRoot, config, fs }) => {
+    const result = await verifyVersionAlignment({ projectRoot, config, fs });
+    return {
+        gate: 'version-alignment',
+        passed: true, // Advisory — always passes
+        errors: result.errors,
+        warnings: result.warnings,
+    };
+};
 // Register built-in gates
 registerGate('frontmatter', frontmatterGate);
 registerGate('triplets', tripletsGate);
@@ -102,6 +132,9 @@ registerGate('freshness', freshnessGate);
 registerGate('invariant-coverage', invariantCoverageGate);
 registerGate('workflow-quality', workflowQualityGate);
 registerGate('tier4-tests', tier4TestsGate);
+registerGate('placeholder-detection', placeholderDetectionGate);
+registerGate('references', referencesGate);
+registerGate('version-alignment', versionAlignmentGate);
 // ---------------------------------------------------------------------------
 // Main
 // ---------------------------------------------------------------------------

package/dist/core/verify.js.map

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package/dist/templates/config.d.ts

@@ -1,6 +1,6 @@
 /**
  * organon.config.json template for organon init.
  */
-export declare const CONFIG_TEMPLATE = "{\n  \"methodology_version\": \"0.3.0\",\n  \"organonPaths\": [\"organon\", \".\"],\n  \"organonGlobs\": [\n    \"**/ETHOS.md\",\n    \"**/PHILOSOPHY.md\",\n    \"**/PROTOCOL.md\",\n    \"**/PROTOCOLS.md\",\n    \"**/README.md\",\n    \"**/components.md\"\n  ],\n  \"ignorePatterns\": [\n    \"**/node_modules/**\",\n    \"**/dist/**\",\n    \"**/.git/**\",\n    \"**/coverage/**\"\n  ],\n  \"workflowPaths\": {\n    \"claudeCode\": \".claude/skills\",\n    \"cursor\": \".cursor/rules\",\n    \"generic\": \"organon/workflows\"\n  },\n  \"freshnessThresholdHours\": 720\n}\n";
-export declare const METHODOLOGY_VERSION = "0.3.0";
+export declare const CONFIG_TEMPLATE = "{\n  \"methodology_version\": \"0.4.1\",\n  \"organonPaths\": [\"organon\", \".\"],\n  \"organonGlobs\": [\n    \"**/ETHOS.md\",\n    \"**/PHILOSOPHY.md\",\n    \"**/PROTOCOL.md\",\n    \"**/PROTOCOLS.md\",\n    \"**/README.md\",\n    \"**/PRIMER.md\",\n    \"**/methodology-reference.md\",\n    \"**/components.md\"\n  ],\n  \"ignorePatterns\": [\n    \"**/node_modules/**\",\n    \"**/dist/**\",\n    \"**/.git/**\",\n    \"**/coverage/**\"\n  ],\n  \"workflowPaths\": {\n    \"claudeCode\": \".claude/skills\",\n    \"cursor\": \".cursor/rules\",\n    \"generic\": \"organon/workflows\"\n  },\n  \"freshnessThresholdHours\": 720,\n  \"testGlobs\": [\n    \"**/*.test.ts\",\n    \"**/*.test.js\",\n    \"**/*.spec.ts\",\n    \"**/*.spec.js\"\n  ],\n  \"testIgnorePatterns\": [\n    \"**/node_modules/**\",\n    \"**/dist/**\"\n  ]\n}\n";
+export declare const METHODOLOGY_VERSION = "0.4.1";
 //# sourceMappingURL=config.d.ts.map

package/dist/templates/config.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"config.d.ts","sourceRoot":"","sources":["../../src/templates/config.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,eAAO,MAAM,eAAe,00BAoC3B,CAAC;AAEF,eAAO,MAAM,mBAAmB,UAAU,CAAC"}