@organon-methodology/tools 0.3.0

package/dist/core/health.js

@@ -0,0 +1,156 @@
+/**
+ * Health dashboard.
+ *
+ * Reports coverage (% files with frontmatter), validation status,
+ * token analysis, freshness, and overall health score.
+ */
+import { estimateTokens, parseOrganonFile } from './frontmatter-parser.js';
+import { validateFrontmatter } from './validate-frontmatter.js';
+import { joinPath } from './config.js';
+// ---------------------------------------------------------------------------
+// Main
+// ---------------------------------------------------------------------------
+export async function health(options) {
+    const { projectRoot, config, fs } = options;
+    const errors = [];
+    const warnings = [];
+    const issues = [];
+    // Discover organon files
+    const allFiles = await discoverOrganonFiles(projectRoot, config, fs);
+    // Parse all files
+    const parsed = [];
+    for (const file of allFiles) {
+        const absPath = joinPath(projectRoot, file);
+        try {
+            const content = await fs.readFile(absPath);
+            parsed.push(parseOrganonFile(file, content));
+        }
+        catch {
+            errors.push({
+                severity: 'error',
+                code: 'FILE_READ_ERROR',
+                message: `Cannot read file: ${file}`,
+                file,
+            });
+        }
+    }
+    // Coverage
+    const withFrontmatter = parsed.filter((f) => f.frontmatter !== null);
+    const coverage = {
+        totalFiles: parsed.length,
+        withFrontmatter: withFrontmatter.length,
+        percentage: parsed.length > 0 ? Math.round((withFrontmatter.length / parsed.length) * 100) : 0,
+    };
+    if (coverage.percentage < 100) {
+        const missingFiles = parsed.filter((f) => f.frontmatter === null);
+        for (const f of missingFiles) {
+            issues.push({
+                severity: 'warning',
+                code: 'HEALTH_MISSING_FRONTMATTER',
+                message: `Missing frontmatter: ${f.path}`,
+                file: f.path,
+                suggestion: options.fixSuggestions ? 'Run: organon generate <file>' : undefined,
+            });
+        }
+    }
+    // Validation
+    const validationResult = await validateFrontmatter({
+        projectRoot,
+        config,
+        fs,
+        stages: [1, 3], // Schema + truthfulness only (faster than full validation)
+    });
+    const validation = {
+        passing: validationResult.filesChecked - validationResult.filesWithErrors,
+        failing: validationResult.filesWithErrors,
+        warnings: validationResult.filesWithWarnings,
+    };
+    // Push validation issues
+    for (const r of validationResult.results) {
+        for (const e of r.errors)
+            issues.push(e);
+        for (const w of r.warnings)
+            issues.push(w);
+    }
+    // Token analysis
+    const tokenEstimates = withFrontmatter
+        .map((f) => ({ file: f.path, tokens: f.frontmatter.token_estimate ?? estimateTokens(f.content) }))
+        .sort((a, b) => b.tokens - a.tokens);
+    const totalTokens = tokenEstimates.reduce((sum, t) => sum + t.tokens, 0);
+    const tokens = {
+        total: totalTokens,
+        average: tokenEstimates.length > 0 ? Math.round(totalTokens / tokenEstimates.length) : 0,
+        largest: tokenEstimates.length > 0 ? tokenEstimates[0] : { file: '', tokens: 0 },
+        smallest: tokenEstimates.length > 0 ? tokenEstimates[tokenEstimates.length - 1] : { file: '', tokens: 0 },
+    };
+    // Freshness
+    const now = new Date();
+    const thresholdMs = config.freshnessThresholdHours * 60 * 60 * 1000;
+    let fresh = 0;
+    let stale = 0;
+    let unknown = 0;
+    let stalestFile;
+    for (const file of allFiles) {
+        const absPath = joinPath(projectRoot, file);
+        try {
+            const stat = await fs.stat(absPath);
+            const ageMs = now.getTime() - stat.mtime.getTime();
+            if (ageMs > thresholdMs) {
+                stale++;
+                if (!stalestFile || stat.mtime < stalestFile.lastModified) {
+                    stalestFile = { file, lastModified: stat.mtime };
+                }
+            }
+            else {
+                fresh++;
+            }
+        }
+        catch {
+            unknown++;
+        }
+    }
+    const freshness = { fresh, stale, unknown, stalestFile };
+    // Score calculation (0-100)
+    const coverageScore = coverage.percentage; // 0-100
+    const validationScore = validationResult.filesChecked > 0
+        ? Math.round(((validationResult.filesChecked - validationResult.filesWithErrors) / validationResult.filesChecked) * 100)
+        : 100;
+    const freshnessScore = allFiles.length > 0
+        ? Math.round((fresh / allFiles.length) * 100)
+        : 100;
+    // Weighted average: coverage 40%, validation 40%, freshness 20%
+    const score = Math.round(coverageScore * 0.4 +
+        validationScore * 0.4 +
+        freshnessScore * 0.2);
+    return {
+        success: errors.length === 0,
+        score,
+        coverage,
+        validation,
+        tokens,
+        freshness,
+        issues,
+        errors,
+        warnings,
+    };
+}
+// ---------------------------------------------------------------------------
+// Helpers
+// ---------------------------------------------------------------------------
+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=health.js.map

package/dist/core/health.js.map

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

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

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

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+{"version":3,"file":"health.test.d.ts","sourceRoot":"","sources":["../../src/core/health.test.ts"],"names":[],"mappings":""}

package/dist/core/health.test.js

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+import { describe, it, expect } from 'vitest';
+import { health } from './health.js';
+import { MemoryFileSystem, makeEthos, makeReadme } from './test-helpers.js';
+function makeConfig(projectRoot) {
+    return {
+        projectRoot,
+        organonPaths: ['.'],
+        organonGlobs: ['**/ETHOS.md', '**/README.md'],
+        ignorePatterns: [],
+        workflowPaths: {},
+        freshnessThresholdHours: 24,
+    };
+}
+describe('health', () => {
+    it('reports 100% coverage when all files have frontmatter', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/ETHOS.md': makeEthos({ name: 'test', scope: 'product' }),
+            '/project/README.md': makeReadme({ name: 'root', scope: 'product' }),
+        });
+        const config = makeConfig('/project');
+        const result = await health({ projectRoot: '/project', config, fs });
+        expect(result.coverage.percentage).toBe(100);
+    });
+    it('reports partial coverage', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/ETHOS.md': makeEthos({ name: 'test', scope: 'product' }),
+            '/project/README.md': '# No frontmatter here',
+        });
+        const config = makeConfig('/project');
+        const result = await health({ projectRoot: '/project', config, fs });
+        expect(result.coverage.percentage).toBe(50);
+        expect(result.coverage.withFrontmatter).toBe(1);
+        expect(result.coverage.totalFiles).toBe(2);
+    });
+    it('calculates a health score', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/ETHOS.md': makeEthos({ name: 'test', scope: 'product' }),
+        });
+        const config = makeConfig('/project');
+        const result = await health({ projectRoot: '/project', config, fs });
+        expect(result.score).toBeGreaterThanOrEqual(0);
+        expect(result.score).toBeLessThanOrEqual(100);
+    });
+    it('includes token analysis', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/ETHOS.md': makeEthos({ name: 'test', scope: 'product' }),
+        });
+        const config = makeConfig('/project');
+        const result = await health({ projectRoot: '/project', config, fs });
+        expect(result.tokens.total).toBeGreaterThan(0);
+        expect(result.tokens.average).toBeGreaterThan(0);
+        expect(result.tokens.largest.file).toBeTruthy();
+    });
+    it('reports freshness', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/ETHOS.md': makeEthos({ name: 'test', scope: 'product' }),
+        });
+        const config = makeConfig('/project');
+        const result = await health({ projectRoot: '/project', config, fs });
+        expect(result.freshness.fresh + result.freshness.stale + result.freshness.unknown)
+            .toBe(1);
+    });
+    it('detects stale files', async () => {
+        const fs = new MemoryFileSystem();
+        // Add file with old mtime
+        const oldDate = new Date(Date.now() - 48 * 60 * 60 * 1000); // 48h ago
+        fs.addFile('/project/ETHOS.md', makeEthos({ name: 'test', scope: 'product' }), oldDate);
+        const config = makeConfig('/project');
+        const result = await health({ projectRoot: '/project', config, fs });
+        expect(result.freshness.stale).toBe(1);
+        expect(result.freshness.stalestFile).toBeTruthy();
+    });
+    it('includes fix suggestions when requested', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/ETHOS.md': makeEthos({ name: 'test', scope: 'product' }),
+            '/project/README.md': '# No frontmatter',
+        });
+        const config = makeConfig('/project');
+        const result = await health({
+            projectRoot: '/project',
+            config,
+            fs,
+            fixSuggestions: true,
+        });
+        const missing = result.issues.find((i) => i.code === 'HEALTH_MISSING_FRONTMATTER');
+        expect(missing?.suggestion).toBeTruthy();
+    });
+    it('gives high score for perfect project', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/ETHOS.md': makeEthos({ name: 'test', scope: 'product' }),
+        });
+        const config = makeConfig('/project');
+        const result = await health({ projectRoot: '/project', config, fs });
+        expect(result.score).toBeGreaterThanOrEqual(80);
+    });
+});
+//# sourceMappingURL=health.test.js.map

package/dist/core/health.test.js.map

@@ -0,0 +1 @@
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package/dist/core/init.d.ts

@@ -0,0 +1,25 @@
+/**
+ * Pure init logic for `organon init`.
+ *
+ * Returns a file tree as Map<string, string> (path → content).
+ * Never writes directly — the CLI handler applies the result.
+ *
+ * @organon-invariant INV-TOOLS-5 idempotent-operations
+ */
+import type { FileSystem, DiagnosticMessage } from './types.js';
+export interface InitOptions {
+    projectRoot: string;
+    installSkills: boolean;
+    force: boolean;
+    fs: FileSystem;
+}
+export interface InitResult {
+    success: boolean;
+    /** Files to create: relative path → content */
+    files: Map<string, string>;
+    /** Files skipped because they already exist (and --force not set) */
+    skipped: string[];
+    diagnostics: DiagnosticMessage[];
+}
+export declare function init(options: InitOptions): Promise<InitResult>;
+//# sourceMappingURL=init.d.ts.map

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

@@ -0,0 +1 @@
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package/dist/core/init.js

@@ -0,0 +1,100 @@
+/**
+ * Pure init logic for `organon init`.
+ *
+ * Returns a file tree as Map<string, string> (path → content).
+ * Never writes directly — the CLI handler applies the result.
+ *
+ * @organon-invariant INV-TOOLS-5 idempotent-operations
+ */
+import { joinPath } from './config.js';
+import { getSkillTemplates, ETHOS_TEMPLATE, PHILOSOPHY_TEMPLATE, README_TEMPLATE, PROTOCOLS_TEMPLATE, CLAUDE_MD_TEMPLATE, OBSERVATIONS_README_TEMPLATE, CONFIG_TEMPLATE, } from '../templates/index.js';
+// ---------------------------------------------------------------------------
+// Main
+// ---------------------------------------------------------------------------
+export async function init(options) {
+    const { projectRoot, installSkills, force, fs } = options;
+    const files = new Map();
+    const skipped = [];
+    const diagnostics = [];
+    // 1. Generate organon scaffold files
+    const organonFiles = [
+        ['organon.config.json', CONFIG_TEMPLATE],
+        ['CLAUDE.md', CLAUDE_MD_TEMPLATE],
+        ['organon/ETHOS.md', ETHOS_TEMPLATE],
+        ['organon/PHILOSOPHY.md', PHILOSOPHY_TEMPLATE],
+        ['organon/README.md', README_TEMPLATE],
+        ['organon/protocols/PROTOCOLS.md', PROTOCOLS_TEMPLATE],
+        ['organon/observations/README.md', OBSERVATIONS_README_TEMPLATE],
+    ];
+    for (const [relativePath, content] of organonFiles) {
+        try {
+            const fullPath = joinPath(projectRoot, relativePath);
+            const exists = await fs.exists(fullPath);
+            if (exists && !force) {
+                skipped.push(relativePath);
+                diagnostics.push({
+                    severity: 'info',
+                    code: 'INIT_FILE_EXISTS',
+                    message: `Skipped (already exists): ${relativePath}`,
+                    file: relativePath,
+                });
+            }
+            else {
+                files.set(relativePath, content);
+            }
+        }
+        catch (err) {
+            diagnostics.push({
+                severity: 'error',
+                code: 'INIT_CHECK_ERROR',
+                message: `Could not check ${relativePath}: ${err instanceof Error ? err.message : String(err)}`,
+                file: relativePath,
+            });
+        }
+    }
+    // 2. Generate skill files (if requested)
+    if (installSkills) {
+        const skillTemplates = getSkillTemplates();
+        for (const [, { path: relativePath, content }] of skillTemplates) {
+            try {
+                const fullPath = joinPath(projectRoot, relativePath);
+                const exists = await fs.exists(fullPath);
+                if (exists && !force) {
+                    skipped.push(relativePath);
+                    diagnostics.push({
+                        severity: 'info',
+                        code: 'INIT_SKILL_EXISTS',
+                        message: `Skipped skill (already exists): ${relativePath}`,
+                        file: relativePath,
+                    });
+                }
+                else {
+                    files.set(relativePath, content);
+                }
+            }
+            catch (err) {
+                diagnostics.push({
+                    severity: 'error',
+                    code: 'INIT_CHECK_ERROR',
+                    message: `Could not check ${relativePath}: ${err instanceof Error ? err.message : String(err)}`,
+                    file: relativePath,
+                });
+            }
+        }
+    }
+    // 3. Summary diagnostic
+    if (files.size === 0 && skipped.length > 0) {
+        diagnostics.push({
+            severity: 'info',
+            code: 'INIT_ALREADY_INITIALIZED',
+            message: `Project already initialized. All ${skipped.length} files exist. Use --force to overwrite.`,
+        });
+    }
+    return {
+        success: diagnostics.filter((d) => d.severity === 'error').length === 0,
+        files,
+        skipped,
+        diagnostics,
+    };
+}
+//# sourceMappingURL=init.js.map

package/dist/core/init.js.map

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

@@ -0,0 +1,8 @@
+/**
+ * Tests for organon init core logic.
+ *
+ * @organon-invariant INV-TOOLS-2 every-command-has-tests
+ * @organon-invariant INV-TOOLS-5 idempotent-operations
+ */
+export {};
+//# sourceMappingURL=init.test.d.ts.map

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

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

package/dist/core/init.test.js

@@ -0,0 +1,203 @@
+/**
+ * Tests for organon init core logic.
+ *
+ * @organon-invariant INV-TOOLS-2 every-command-has-tests
+ * @organon-invariant INV-TOOLS-5 idempotent-operations
+ */
+import { describe, it, expect } from 'vitest';
+import { init } from './init.js';
+import { MemoryFileSystem } from './test-helpers.js';
+import { getSkillTemplates, METHODOLOGY_VERSION } from '../templates/index.js';
+describe('init', () => {
+    it('generates all organon scaffold files', async () => {
+        const fs = new MemoryFileSystem();
+        const result = await init({
+            projectRoot: '/project',
+            installSkills: false,
+            force: false,
+            fs,
+        });
+        expect(result.success).toBe(true);
+        expect(result.files.size).toBeGreaterThanOrEqual(7);
+        expect(result.files.has('organon.config.json')).toBe(true);
+        expect(result.files.has('CLAUDE.md')).toBe(true);
+        expect(result.files.has('organon/ETHOS.md')).toBe(true);
+        expect(result.files.has('organon/PHILOSOPHY.md')).toBe(true);
+        expect(result.files.has('organon/README.md')).toBe(true);
+        expect(result.files.has('organon/protocols/PROTOCOLS.md')).toBe(true);
+        expect(result.files.has('organon/observations/README.md')).toBe(true);
+    });
+    it('generates skill files when installSkills is true', async () => {
+        const fs = new MemoryFileSystem();
+        const result = await init({
+            projectRoot: '/project',
+            installSkills: true,
+            force: false,
+            fs,
+        });
+        expect(result.success).toBe(true);
+        expect(result.files.size).toBe(7 + getSkillTemplates().size);
+        expect(result.files.has('.claude/skills/domain-feature-design/SKILL.md')).toBe(true);
+        expect(result.files.has('.claude/skills/organon-file-creation/SKILL.md')).toBe(true);
+        expect(result.files.has('.claude/skills/quality-review/SKILL.md')).toBe(true);
+        expect(result.files.has('.claude/skills/session-compounding/SKILL.md')).toBe(true);
+        expect(result.files.has('.claude/skills/verify-and-health/SKILL.md')).toBe(true);
+    });
+    it('skips existing files without --force', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/organon/ETHOS.md': '# Existing ethos',
+            '/project/organon.config.json': '{}',
+        });
+        const result = await init({
+            projectRoot: '/project',
+            installSkills: false,
+            force: false,
+            fs,
+        });
+        expect(result.success).toBe(true);
+        expect(result.skipped).toContain('organon/ETHOS.md');
+        expect(result.skipped).toContain('organon.config.json');
+        expect(result.files.has('organon/ETHOS.md')).toBe(false);
+        expect(result.files.has('organon.config.json')).toBe(false);
+        // Other files still generated
+        expect(result.files.has('organon/PHILOSOPHY.md')).toBe(true);
+    });
+    it('overwrites existing files with --force', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/organon/ETHOS.md': '# Existing ethos',
+        });
+        const result = await init({
+            projectRoot: '/project',
+            installSkills: false,
+            force: true,
+            fs,
+        });
+        expect(result.success).toBe(true);
+        expect(result.skipped.length).toBe(0);
+        expect(result.files.has('organon/ETHOS.md')).toBe(true);
+    });
+    it('reports already-initialized when all files exist', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/organon.config.json': '{}',
+            '/project/CLAUDE.md': '# claude',
+            '/project/organon/ETHOS.md': '# ethos',
+            '/project/organon/PHILOSOPHY.md': '# phil',
+            '/project/organon/README.md': '# readme',
+            '/project/organon/protocols/PROTOCOLS.md': '# protocols',
+            '/project/organon/observations/README.md': '# observations',
+        });
+        const result = await init({
+            projectRoot: '/project',
+            installSkills: false,
+            force: false,
+            fs,
+        });
+        expect(result.success).toBe(true);
+        expect(result.files.size).toBe(0);
+        expect(result.skipped.length).toBe(7);
+        const codes = result.diagnostics.map((d) => d.code);
+        expect(codes).toContain('INIT_ALREADY_INITIALIZED');
+    });
+    it('generates files with valid frontmatter', async () => {
+        const fs = new MemoryFileSystem();
+        const result = await init({
+            projectRoot: '/project',
+            installSkills: false,
+            force: false,
+            fs,
+        });
+        // Check that generated organon files have YAML frontmatter delimiters
+        // CLAUDE.md is not an organon file, so it doesn't need frontmatter
+        for (const [filePath, content] of result.files) {
+            if (filePath.endsWith('.md') && filePath !== 'CLAUDE.md') {
+                expect(content.startsWith('---\n'), `${filePath} should start with frontmatter`).toBe(true);
+                expect(content.includes('\n---\n'), `${filePath} should have closing frontmatter`).toBe(true);
+            }
+        }
+    });
+    it('generated config has methodology_version', async () => {
+        const fs = new MemoryFileSystem();
+        const result = await init({
+            projectRoot: '/project',
+            installSkills: false,
+            force: false,
+            fs,
+        });
+        const configContent = result.files.get('organon.config.json');
+        expect(configContent).toBeDefined();
+        const config = JSON.parse(configContent);
+        expect(config.methodology_version).toBe(METHODOLOGY_VERSION);
+    });
+    it('skill templates have methodology_version in frontmatter', async () => {
+        const fs = new MemoryFileSystem();
+        const result = await init({
+            projectRoot: '/project',
+            installSkills: true,
+            force: false,
+            fs,
+        });
+        for (const [path, content] of result.files) {
+            if (path.includes('.claude/skills/')) {
+                expect(content).toContain(`methodology_version: "${METHODOLOGY_VERSION}"`);
+                expect(content).toContain('protocol_id:');
+                expect(content).toContain('protocol_file:');
+            }
+        }
+    });
+    it('is idempotent — second run skips all files created by first', async () => {
+        const fs = new MemoryFileSystem();
+        // First run: generates all files
+        const result1 = await init({
+            projectRoot: '/project',
+            installSkills: true,
+            force: false,
+            fs,
+        });
+        expect(result1.files.size).toBeGreaterThan(0);
+        // Simulate writing the files to the FS
+        for (const [relativePath, content] of result1.files) {
+            fs.addFile(`/project/${relativePath}`, content);
+        }
+        // Second run: all files already exist, should skip everything
+        const result2 = await init({
+            projectRoot: '/project',
+            installSkills: true,
+            force: false,
+            fs,
+        });
+        expect(result2.files.size).toBe(0);
+        expect(result2.skipped.length).toBe(result1.files.size);
+    });
+    it('emits error diagnostic when fs.exists throws for organon files', async () => {
+        const fs = new MemoryFileSystem();
+        fs.throwOn('ETHOS.md');
+        const result = await init({
+            projectRoot: '/project',
+            installSkills: false,
+            force: false,
+            fs,
+        });
+        expect(result.success).toBe(false);
+        const errorDiags = result.diagnostics.filter((d) => d.severity === 'error');
+        expect(errorDiags.length).toBeGreaterThan(0);
+        expect(errorDiags.some((d) => d.code === 'INIT_CHECK_ERROR')).toBe(true);
+        // Other files not affected by the throw should still be generated
+        expect(result.files.has('organon/PHILOSOPHY.md')).toBe(true);
+    });
+    it('emits error diagnostic when fs.exists throws for skill files', async () => {
+        const fs = new MemoryFileSystem();
+        fs.throwOn('verify-and-health');
+        const result = await init({
+            projectRoot: '/project',
+            installSkills: true,
+            force: false,
+            fs,
+        });
+        expect(result.success).toBe(false);
+        const errorDiags = result.diagnostics.filter((d) => d.severity === 'error');
+        expect(errorDiags.some((d) => d.code === 'INIT_CHECK_ERROR' && d.file?.includes('verify-and-health'))).toBe(true);
+        // Other skills should still be generated
+        expect(result.files.has('.claude/skills/quality-review/SKILL.md')).toBe(true);
+    });
+});
+//# sourceMappingURL=init.test.js.map

package/dist/core/init.test.js.map

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