@organon-methodology/tools 0.3.0

package/dist/core/verify-triplets.js

@@ -0,0 +1,217 @@
+/**
+ * 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 { parseFrontmatter } from './frontmatter-parser.js';
+import { joinPath } from './config.js';
+// ---------------------------------------------------------------------------
+// Main
+// ---------------------------------------------------------------------------
+export async function verifyTriplets(options) {
+    const { projectRoot, config, fs } = options;
+    const errors = [];
+    const warnings = [];
+    // Discover protocol files (type: procedures)
+    const organonFiles = await discoverOrganonFiles(projectRoot, config, fs);
+    const protocolFiles = [];
+    const allFrontmatter = new Map();
+    for (const file of organonFiles) {
+        const absPath = joinPath(projectRoot, file);
+        try {
+            const content = await fs.readFile(absPath);
+            const { frontmatter, body } = parseFrontmatter(content);
+            allFrontmatter.set(file, frontmatter);
+            if (frontmatter?.type === 'procedures') {
+                protocolFiles.push({ path: file, frontmatter, rawFrontmatter: '', body, content });
+            }
+        }
+        catch {
+            errors.push({
+                severity: 'error',
+                code: 'FILE_READ_ERROR',
+                message: `Cannot read file: ${file}`,
+                file,
+            });
+        }
+    }
+    // Discover workflow files
+    const workflowFiles = await discoverWorkflowFiles(projectRoot, config, fs);
+    const workflowFrontmatter = new Map();
+    for (const wf of workflowFiles) {
+        const absPath = joinPath(projectRoot, wf);
+        try {
+            const content = await fs.readFile(absPath);
+            const { frontmatter } = parseFrontmatter(content);
+            if (frontmatter) {
+                workflowFrontmatter.set(wf, {
+                    protocolId: frontmatter['protocol_id'],
+                    protocolFile: frontmatter['protocol_file'],
+                });
+            }
+            else {
+                // Try to extract protocol_id from body (some workflows use inline metadata)
+                const protoMatch = content.match(/protocol[_\s]?id\s*:\s*(\S+)/i);
+                const protoFileMatch = content.match(/protocol[_\s]?file\s*:\s*(\S+)/i);
+                workflowFrontmatter.set(wf, {
+                    protocolId: protoMatch ? protoMatch[1] : undefined,
+                    protocolFile: protoFileMatch ? protoFileMatch[1] : undefined,
+                });
+            }
+        }
+        catch {
+            // Workflow file unreadable — will surface as orphan check issue
+        }
+    }
+    // Build bindings from protocol entries
+    const bindings = [];
+    const referencedWorkflows = new Set();
+    for (const pf of protocolFiles) {
+        if (!pf.frontmatter?.protocols)
+            continue;
+        for (const proto of pf.frontmatter.protocols) {
+            const bindingIssues = [];
+            let valid = true;
+            if (proto.automation_tier === 'automated') {
+                if (!proto.workflow) {
+                    valid = false;
+                    bindingIssues.push({
+                        severity: 'error',
+                        code: 'TRIPLET_MISSING_WORKFLOW_NAME',
+                        message: `Protocol ${proto.id} is automated but has no workflow field`,
+                        file: pf.path,
+                        suggestion: `Add 'workflow: <name>' to protocol ${proto.id}`,
+                    });
+                }
+                else {
+                    referencedWorkflows.add(proto.workflow);
+                    // Find the workflow file
+                    const wfFile = findWorkflowFile(proto.workflow, workflowFiles);
+                    if (!wfFile) {
+                        valid = false;
+                        bindingIssues.push({
+                            severity: 'error',
+                            code: 'TRIPLET_WORKFLOW_NOT_FOUND',
+                            message: `Protocol ${proto.id} references workflow '${proto.workflow}' but no matching file found`,
+                            file: pf.path,
+                            suggestion: `Create workflow file for '${proto.workflow}'`,
+                        });
+                    }
+                    else {
+                        // Check bidirectional reference
+                        const wfData = workflowFrontmatter.get(wfFile);
+                        if (wfData && wfData.protocolId !== proto.id) {
+                            valid = false;
+                            bindingIssues.push({
+                                severity: 'error',
+                                code: 'TRIPLET_BACK_REFERENCE_MISMATCH',
+                                message: `Workflow '${wfFile}' has protocol_id '${wfData.protocolId ?? 'none'}' but expected '${proto.id}'`,
+                                file: wfFile,
+                                suggestion: `Update protocol_id in '${wfFile}' to '${proto.id}'`,
+                            });
+                        }
+                    }
+                }
+            }
+            bindings.push({
+                protocolId: proto.id,
+                protocolFile: pf.path,
+                automationTier: proto.automation_tier,
+                workflowName: proto.workflow,
+                workflowFile: proto.workflow ? findWorkflowFile(proto.workflow, workflowFiles) ?? undefined : undefined,
+                tools: proto.tools,
+                valid,
+                issues: bindingIssues,
+            });
+            errors.push(...bindingIssues.filter((i) => i.severity === 'error'));
+            warnings.push(...bindingIssues.filter((i) => i.severity === 'warning'));
+        }
+    }
+    // Find orphaned workflows (workflow files not referenced by any protocol)
+    const orphanedWorkflows = [];
+    for (const wf of workflowFiles) {
+        const wfData = workflowFrontmatter.get(wf);
+        if (wfData?.protocolId) {
+            // Check if any protocol actually has this ID
+            const referenced = bindings.some((b) => b.protocolId === wfData.protocolId);
+            if (!referenced) {
+                orphanedWorkflows.push(wf);
+                warnings.push({
+                    severity: 'warning',
+                    code: 'TRIPLET_ORPHANED_WORKFLOW',
+                    message: `Workflow '${wf}' references protocol_id '${wfData.protocolId}' but no matching protocol found`,
+                    file: wf,
+                });
+            }
+        }
+    }
+    // Find phantom automation (protocol claims automated but no workflow exists anywhere)
+    const phantomAutomation = bindings
+        .filter((b) => b.automationTier === 'automated' && !b.valid)
+        .map((b) => b.protocolId);
+    return {
+        success: errors.length === 0,
+        bindings,
+        orphanedWorkflows,
+        phantomAutomation,
+        errors,
+        warnings,
+    };
+}
+// ---------------------------------------------------------------------------
+// Helpers
+// ---------------------------------------------------------------------------
+function findWorkflowFile(workflowName, workflowFiles) {
+    const normalized = workflowName.toLowerCase().replace(/[^a-z0-9]/g, '-');
+    for (const wf of workflowFiles) {
+        const wfNormalized = wf.replace(/\\/g, '/').toLowerCase();
+        if (wfNormalized.includes(normalized) ||
+            wfNormalized.includes(workflowName.toLowerCase())) {
+            return wf;
+        }
+    }
+    return null;
+}
+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();
+}
+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

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

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

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

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

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

@@ -0,0 +1,147 @@
+import { describe, it, expect } from 'vitest';
+import { verifyTriplets } from './verify-triplets.js';
+import { MemoryFileSystem } from './test-helpers.js';
+function makeConfig(projectRoot) {
+    return {
+        projectRoot,
+        organonPaths: ['.'],
+        organonGlobs: ['**/ETHOS.md', '**/PROTOCOL.md', '**/PROTOCOLS.md'],
+        ignorePatterns: [],
+        workflowPaths: { generic: 'workflows' },
+        freshnessThresholdHours: 24,
+    };
+}
+describe('verifyTriplets', () => {
+    it('passes when automated protocols have valid workflow bindings', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/PROTOCOLS.md': `---
+type: procedures
+scope: methodology
+name: test-protocols
+version: "1.0"
+summary: Test
+token_estimate: 300
+protocols_count: 1
+protocols:
+  - id: PROTO-TEST-1
+    name: Test Protocol
+    steps: 6
+    automation_tier: automated
+    workflow: test-workflow
+    complexity: high
+---
+
+## Steps
+1. Do thing.`,
+            '/project/workflows/test-workflow.md': `---
+protocol_id: PROTO-TEST-1
+protocol_file: PROTOCOLS.md
+---
+
+# Test Workflow`,
+        });
+        const config = makeConfig('/project');
+        const result = await verifyTriplets({ projectRoot: '/project', config, fs });
+        expect(result.bindings.length).toBe(1);
+        expect(result.bindings[0].valid).toBe(true);
+        expect(result.phantomAutomation).toHaveLength(0);
+    });
+    it('detects phantom automation (protocol automated but no workflow)', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/PROTOCOLS.md': `---
+type: procedures
+scope: methodology
+name: test-protocols
+version: "1.0"
+summary: Test
+token_estimate: 300
+protocols_count: 1
+protocols:
+  - id: PROTO-TEST-1
+    name: Test Protocol
+    steps: 6
+    automation_tier: automated
+    workflow: nonexistent-workflow
+    complexity: high
+---
+
+## Steps
+1. Do thing.`,
+        });
+        const config = makeConfig('/project');
+        const result = await verifyTriplets({ projectRoot: '/project', config, fs });
+        expect(result.success).toBe(false);
+        expect(result.phantomAutomation).toContain('PROTO-TEST-1');
+    });
+    it('detects missing workflow field for automated protocol', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/PROTOCOLS.md': `---
+type: procedures
+scope: methodology
+name: test-protocols
+version: "1.0"
+summary: Test
+token_estimate: 300
+protocols_count: 1
+protocols:
+  - id: PROTO-TEST-1
+    name: Test Protocol
+    steps: 6
+    automation_tier: automated
+    complexity: high
+---
+
+## Steps
+1. Do thing.`,
+        });
+        const config = makeConfig('/project');
+        const result = await verifyTriplets({ projectRoot: '/project', config, fs });
+        expect(result.success).toBe(false);
+        expect(result.errors).toContainEqual(expect.objectContaining({ code: 'TRIPLET_MISSING_WORKFLOW_NAME' }));
+    });
+    it('passes for manual protocols without workflows', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/PROTOCOLS.md': `---
+type: procedures
+scope: methodology
+name: test-protocols
+version: "1.0"
+summary: Test
+token_estimate: 300
+protocols_count: 1
+protocols:
+  - id: PROTO-TEST-1
+    name: Manual Protocol
+    steps: 3
+    automation_tier: manual
+    complexity: low
+---
+
+## Steps
+1. Do thing.`,
+        });
+        const config = makeConfig('/project');
+        const result = await verifyTriplets({ projectRoot: '/project', config, fs });
+        expect(result.success).toBe(true);
+        expect(result.bindings[0].valid).toBe(true);
+    });
+    it('succeeds when no protocol files exist', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/ETHOS.md': `---
+type: constraints
+scope: product
+name: test
+version: "1.0"
+summary: Test
+token_estimate: 100
+---
+
+# Content`,
+        });
+        const config = makeConfig('/project');
+        const result = await verifyTriplets({ projectRoot: '/project', config, fs });
+        expect(result.success).toBe(true);
+        expect(result.bindings).toHaveLength(0);
+    });
+});
+//# sourceMappingURL=verify-triplets.test.js.map

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

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package/dist/core/verify.d.ts

@@ -0,0 +1,19 @@
+/**
+ * Verification orchestrator with extensible gate registry.
+ *
+ * Built-in gates: frontmatter, triplets, freshness.
+ * Projects can register custom gates via registerGate().
+ * The orchestrator runs all registered gates (or a named subset).
+ */
+import type { FileSystem, OrganonConfig, VerifyGateFn, VerifyResult } from './types.js';
+export interface VerifyOptions {
+    projectRoot: string;
+    config: OrganonConfig;
+    fs: FileSystem;
+    /** Run only these gates. If empty/undefined, runs all registered gates. */
+    gates?: string[];
+}
+export declare function registerGate(name: string, fn: VerifyGateFn): void;
+export declare function getRegisteredGates(): string[];
+export declare function verify(options: VerifyOptions): Promise<VerifyResult>;
+//# sourceMappingURL=verify.d.ts.map

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

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package/dist/core/verify.js

@@ -0,0 +1,162 @@
+/**
+ * Verification orchestrator with extensible gate registry.
+ *
+ * Built-in gates: frontmatter, triplets, freshness.
+ * Projects can register custom gates via registerGate().
+ * The orchestrator runs all registered gates (or a named subset).
+ */
+import { validateFrontmatter } from './validate-frontmatter.js';
+import { verifyTriplets } from './verify-triplets.js';
+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';
+// ---------------------------------------------------------------------------
+// Gate registry
+// ---------------------------------------------------------------------------
+const gateRegistry = new Map();
+export function registerGate(name, fn) {
+    gateRegistry.set(name, fn);
+}
+export function getRegisteredGates() {
+    return [...gateRegistry.keys()];
+}
+// ---------------------------------------------------------------------------
+// Built-in gates
+// ---------------------------------------------------------------------------
+const frontmatterGate = async ({ projectRoot, config, fs }) => {
+    const result = await validateFrontmatter({ projectRoot, config, fs });
+    return {
+        gate: 'frontmatter',
+        passed: result.success,
+        errors: result.errors,
+        warnings: result.warnings,
+    };
+};
+const tripletsGate = async ({ projectRoot, config, fs }) => {
+    const result = await verifyTriplets({ projectRoot, config, fs });
+    return {
+        gate: 'triplets',
+        passed: result.success,
+        errors: result.errors,
+        warnings: result.warnings,
+    };
+};
+const freshnessGate = async ({ projectRoot, config, fs }) => {
+    const result = await runHealth({ projectRoot, config, fs });
+    const errors = [];
+    const warnings = [];
+    if (result.freshness.stale > 0) {
+        warnings.push({
+            severity: 'warning',
+            code: 'FRESHNESS_STALE_FILES',
+            message: `${result.freshness.stale} organon file(s) exceed the freshness threshold of ${config.freshnessThresholdHours}h`,
+        });
+    }
+    if (result.freshness.stalestFile) {
+        warnings.push({
+            severity: 'warning',
+            code: 'FRESHNESS_STALEST',
+            message: `Stalest file: ${result.freshness.stalestFile.file} (last modified: ${result.freshness.stalestFile.lastModified.toISOString()})`,
+            file: result.freshness.stalestFile.file,
+        });
+    }
+    return {
+        gate: 'freshness',
+        passed: true, // Freshness is advisory, not blocking
+        errors,
+        warnings,
+    };
+};
+const invariantCoverageGate = async ({ projectRoot, config, fs }) => {
+    const result = await computeInvariantCoverage({ projectRoot, config, fs });
+    return {
+        gate: 'invariant-coverage',
+        passed: result.success,
+        errors: result.errors,
+        warnings: result.warnings,
+    };
+};
+const workflowQualityGate = async ({ projectRoot, config, fs }) => {
+    const result = await validateWorkflow({ projectRoot, config, fs });
+    return {
+        gate: 'workflow-quality',
+        passed: result.success,
+        errors: result.errors,
+        warnings: result.warnings,
+    };
+};
+const tier4TestsGate = async ({ projectRoot, config, fs }) => {
+    const result = await verifyTier4Tests({ projectRoot, config, fs });
+    return {
+        gate: 'tier4-tests',
+        passed: result.success,
+        errors: result.errors,
+        warnings: result.warnings,
+    };
+};
+// Register built-in gates
+registerGate('frontmatter', frontmatterGate);
+registerGate('triplets', tripletsGate);
+registerGate('freshness', freshnessGate);
+registerGate('invariant-coverage', invariantCoverageGate);
+registerGate('workflow-quality', workflowQualityGate);
+registerGate('tier4-tests', tier4TestsGate);
+// ---------------------------------------------------------------------------
+// Main
+// ---------------------------------------------------------------------------
+export async function verify(options) {
+    const { gates: requestedGates } = options;
+    const allErrors = [];
+    const allWarnings = [];
+    const gateResults = [];
+    const gatesToRun = requestedGates && requestedGates.length > 0
+        ? requestedGates
+        : [...gateRegistry.keys()];
+    for (const gateName of gatesToRun) {
+        const gateFn = gateRegistry.get(gateName);
+        if (!gateFn) {
+            allErrors.push({
+                severity: 'error',
+                code: 'UNKNOWN_GATE',
+                message: `Unknown verification gate: '${gateName}'. Available: ${[...gateRegistry.keys()].join(', ')}`,
+            });
+            continue;
+        }
+        try {
+            const result = await gateFn({
+                projectRoot: options.projectRoot,
+                config: options.config,
+                fs: options.fs,
+            });
+            gateResults.push(result);
+            allErrors.push(...result.errors);
+            allWarnings.push(...result.warnings);
+        }
+        catch (err) {
+            const message = err instanceof Error ? err.message : String(err);
+            gateResults.push({
+                gate: gateName,
+                passed: false,
+                errors: [{
+                        severity: 'error',
+                        code: 'GATE_EXECUTION_ERROR',
+                        message: `Gate '${gateName}' failed: ${message}`,
+                    }],
+                warnings: [],
+            });
+            allErrors.push({
+                severity: 'error',
+                code: 'GATE_EXECUTION_ERROR',
+                message: `Gate '${gateName}' failed: ${message}`,
+            });
+        }
+    }
+    return {
+        success: gateResults.every((g) => g.passed),
+        gates: gateResults,
+        errors: allErrors,
+        warnings: allWarnings,
+    };
+}
+//# sourceMappingURL=verify.js.map

package/dist/core/verify.js.map

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

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

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

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