@organon-methodology/tools 0.3.0 → 0.4.1

package/dist/core/find.test.js

@@ -4,7 +4,7 @@ import { MemoryFileSystem, makeEthos, makeReadme } from './test-helpers.js';
 function makeConfig(projectRoot) {
     return {
         projectRoot,
-        organonPaths: ['.'],
+        organonPaths: ['.', 'organon'],
         organonGlobs: ['**/ETHOS.md', '**/README.md'],
         ignorePatterns: [],
         workflowPaths: {},

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

@@ -1 +1 @@
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package/dist/core/generate-tests.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"generate-tests.d.ts","sourceRoot":"","sources":["../../src/core/generate-tests.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAIH,OAAO,EAGL,KAAK,kBAAkB,EACxB,MAAM,yBAAyB,CAAC;AACjC,OAAO,KAAK,EACV,UAAU,EAEV,aAAa,EACd,MAAM,YAAY,CAAC;AAMpB,MAAM,WAAW,oBAAoB;IACnC,WAAW,EAAE,MAAM,CAAC;IACpB,MAAM,EAAE,aAAa,CAAC;IACtB,EAAE,EAAE,UAAU,CAAC;IACf,oDAAoD;IACpD,YAAY,CAAC,EAAE,MAAM,EAAE,CAAC;IACxB,8CAA8C;IAC9C,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,aAAa;IAC5B,qCAAqC;IACrC,SAAS,EAAE,kBAAkB,CAAC;IAC9B,mCAAmC;IACnC,SAAS,EAAE,MAAM,CAAC;IAClB,mCAAmC;IACnC,IAAI,EAAE,MAAM,CAAC;IACb,yBAAyB;IACzB,QAAQ,EAAE,MAAM,CAAC;CAClB;AAED,MAAM,WAAW,mBAAmB;IAClC,+CAA+C;IAC/C,SAAS,EAAE,aAAa,EAAE,CAAC;IAC3B,iDAAiD;IACjD,cAAc,EAAE,kBAAkB,EAAE,CAAC;IACrC,0CAA0C;IAC1C,aAAa,EAAE,kBAAkB,EAAE,CAAC;CACrC;AA4ID;;GAEG;AACH,wBAAsB,aAAa,CACjC,OAAO,EAAE,oBAAoB,GAC5B,OAAO,CAAC,mBAAmB,CAAC,CAyE9B"}
+{"version":3,"file":"generate-tests.d.ts","sourceRoot":"","sources":["../../src/core/generate-tests.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAKH,OAAO,EAGL,KAAK,kBAAkB,EACxB,MAAM,yBAAyB,CAAC;AACjC,OAAO,KAAK,EACV,UAAU,EAEV,aAAa,EACd,MAAM,YAAY,CAAC;AAMpB,MAAM,WAAW,oBAAoB;IACnC,WAAW,EAAE,MAAM,CAAC;IACpB,MAAM,EAAE,aAAa,CAAC;IACtB,EAAE,EAAE,UAAU,CAAC;IACf,oDAAoD;IACpD,YAAY,CAAC,EAAE,MAAM,EAAE,CAAC;IACxB,8CAA8C;IAC9C,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,aAAa;IAC5B,qCAAqC;IACrC,SAAS,EAAE,kBAAkB,CAAC;IAC9B,mCAAmC;IACnC,SAAS,EAAE,MAAM,CAAC;IAClB,mCAAmC;IACnC,IAAI,EAAE,MAAM,CAAC;IACb,yBAAyB;IACzB,QAAQ,EAAE,MAAM,CAAC;CAClB;AAED,MAAM,WAAW,mBAAmB;IAClC,+CAA+C;IAC/C,SAAS,EAAE,aAAa,EAAE,CAAC;IAC3B,iDAAiD;IACjD,cAAc,EAAE,kBAAkB,EAAE,CAAC;IACrC,0CAA0C;IAC1C,aAAa,EAAE,kBAAkB,EAAE,CAAC;CACrC;AA4ID;;GAEG;AACH,wBAAsB,aAAa,CACjC,OAAO,EAAE,oBAAoB,GAC5B,OAAO,CAAC,mBAAmB,CAAC,CA8D9B"}

package/dist/core/generate-tests.js

@@ -7,6 +7,7 @@
  */
 import { parseFrontmatter } from './frontmatter-parser.js';
 import { joinPath } from './config.js';
+import { discoverOrganonFiles } from './discover.js';
 import { extractInvariants, scanTestAnnotations, } from './invariant-coverage.js';
 function matchAssertion(invariant) {
     const name = invariant.name.toLowerCase();
@@ -129,29 +130,17 @@ describe('${inv.id}', () => {
 export async function generateTests(options) {
     const { projectRoot, config, fs, invariantIds } = options;
     // 1. Discover organon files and extract invariants
-    const seenPaths = new Set();
+    const discoveredFiles = await discoverOrganonFiles(projectRoot, config, fs);
     const parsedFiles = [];
-    for (const organonPath of config.organonPaths) {
-        for (const pattern of config.organonGlobs) {
-            const fullPattern = organonPath === '.' ? pattern : `${organonPath}/${pattern}`;
-            const matches = await fs.glob(fullPattern, {
-                cwd: projectRoot,
-                ignore: config.ignorePatterns,
-            });
-            for (const file of matches) {
-                if (seenPaths.has(file))
-                    continue;
-                seenPaths.add(file);
-                const absPath = joinPath(projectRoot, file);
-                try {
-                    const content = await fs.readFile(absPath);
-                    const { frontmatter } = parseFrontmatter(content);
-                    parsedFiles.push({ path: file, frontmatter });
-                }
-                catch {
-                    // Skip unreadable files
-                }
-            }
+    for (const file of discoveredFiles) {
+        const absPath = joinPath(projectRoot, file);
+        try {
+            const content = await fs.readFile(absPath);
+            const { frontmatter } = parseFrontmatter(content);
+            parsedFiles.push({ path: file, frontmatter });
+        }
+        catch {
+            // Skip unreadable files
         }
     }
     const allInvariants = extractInvariants(parsedFiles);

package/dist/core/generate-tests.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"health.d.ts","sourceRoot":"","sources":["../../src/core/health.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAKH,OAAO,KAAK,EAEV,UAAU,EACV,YAAY,EACZ,aAAa,EAEd,MAAM,YAAY,CAAC;AAMpB,MAAM,WAAW,aAAa;IAC5B,WAAW,EAAE,MAAM,CAAC;IACpB,MAAM,EAAE,aAAa,CAAC;IACtB,EAAE,EAAE,UAAU,CAAC;IACf,wCAAwC;IACxC,cAAc,CAAC,EAAE,OAAO,CAAC;CAC1B;AAMD,wBAAsB,MAAM,CAAC,OAAO,EAAE,aAAa,GAAG,OAAO,CAAC,YAAY,CAAC,CAuI1E"}
+{"version":3,"file":"health.d.ts","sourceRoot":"","sources":["../../src/core/health.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAOH,OAAO,KAAK,EAEV,UAAU,EACV,YAAY,EACZ,aAAa,EAEd,MAAM,YAAY,CAAC;AAMpB,MAAM,WAAW,aAAa;IAC5B,WAAW,EAAE,MAAM,CAAC;IACpB,MAAM,EAAE,aAAa,CAAC;IACtB,EAAE,EAAE,UAAU,CAAC;IACf,wCAAwC;IACxC,cAAc,CAAC,EAAE,OAAO,CAAC;CAC1B;AAMD,wBAAsB,MAAM,CAAC,OAAO,EAAE,aAAa,GAAG,OAAO,CAAC,YAAY,CAAC,CA+I1E"}

package/dist/core/health.js

@@ -6,7 +6,9 @@
  */
 import { estimateTokens, parseOrganonFile } from './frontmatter-parser.js';
 import { validateFrontmatter } from './validate-frontmatter.js';
+import { verifyPlaceholders } from './verify-placeholders.js';
 import { joinPath } from './config.js';
+import { discoverOrganonFiles } from './discover.js';
 // ---------------------------------------------------------------------------
 // Main
 // ---------------------------------------------------------------------------
@@ -110,6 +112,12 @@ export async function health(options) {
         }
     }
     const freshness = { fresh, stale, unknown, stalestFile };
+    // Placeholder penalty (A2): -5 per file with placeholders, capped at -20
+    const placeholderResult = await verifyPlaceholders({ projectRoot, config, fs });
+    const placeholderPenalty = Math.min(placeholderResult.filesWithPlaceholders * 5, 20);
+    for (const pw of placeholderResult.warnings) {
+        issues.push(pw);
+    }
     // Score calculation (0-100)
     const coverageScore = coverage.percentage; // 0-100
     const validationScore = validationResult.filesChecked > 0
@@ -118,10 +126,10 @@ export async function health(options) {
     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 +
+    // Weighted average: coverage 40%, validation 40%, freshness 20%, minus placeholder penalty
+    const score = Math.max(0, Math.round(coverageScore * 0.4 +
         validationScore * 0.4 +
-        freshnessScore * 0.2);
+        freshnessScore * 0.2) - placeholderPenalty);
     return {
         success: errors.length === 0,
         score,
@@ -134,23 +142,4 @@ export async function health(options) {
         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

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

@@ -12,6 +12,8 @@ export interface InitOptions {
     installSkills: boolean;
     force: boolean;
     fs: FileSystem;
+    /** Override auto-detected project name. */
+    projectName?: string;
 }
 export interface InitResult {
     success: boolean;
@@ -21,5 +23,9 @@ export interface InitResult {
     skipped: string[];
     diagnostics: DiagnosticMessage[];
 }
+/**
+ * Detect project name from package.json, Cargo.toml, or directory basename.
+ */
+export declare function detectProjectName(projectRoot: string, fs: FileSystem): Promise<string>;
 export declare function init(options: InitOptions): Promise<InitResult>;
 //# sourceMappingURL=init.d.ts.map

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

@@ -1 +1 @@
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+{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../src/core/init.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,KAAK,EAAE,UAAU,EAAE,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAoBhE,MAAM,WAAW,WAAW;IAC1B,WAAW,EAAE,MAAM,CAAC;IACpB,aAAa,EAAE,OAAO,CAAC;IACvB,KAAK,EAAE,OAAO,CAAC;IACf,EAAE,EAAE,UAAU,CAAC;IACf,2CAA2C;IAC3C,WAAW,CAAC,EAAE,MAAM,CAAC;CACtB;AAED,MAAM,WAAW,UAAU;IACzB,OAAO,EAAE,OAAO,CAAC;IACjB,+CAA+C;IAC/C,KAAK,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAC3B,qEAAqE;IACrE,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,WAAW,EAAE,iBAAiB,EAAE,CAAC;CAClC;AAMD;;GAEG;AACH,wBAAsB,iBAAiB,CACrC,WAAW,EAAE,MAAM,EACnB,EAAE,EAAE,UAAU,GACb,OAAO,CAAC,MAAM,CAAC,CA4BjB;AAoED,wBAAsB,IAAI,CAAC,OAAO,EAAE,WAAW,GAAG,OAAO,CAAC,UAAU,CAAC,CAkGpE"}

package/dist/core/init.js

@@ -6,8 +6,99 @@
  *
  * @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';
+import { joinPath, baseName } from './config.js';
+import { parseFrontmatter } from './frontmatter-parser.js';
+import { getSkillTemplates, ethosTemplate, philosophyTemplate, README_TEMPLATE, PROTOCOLS_TEMPLATE, CLAUDE_MD_TEMPLATE, OBSERVATIONS_README_TEMPLATE, PRIMER_TEMPLATE, METHODOLOGY_REFERENCE_TEMPLATE, CONFIG_TEMPLATE, } from '../templates/index.js';
+// ---------------------------------------------------------------------------
+// Project name detection
+// ---------------------------------------------------------------------------
+/**
+ * Detect project name from package.json, Cargo.toml, or directory basename.
+ */
+export async function detectProjectName(projectRoot, fs) {
+    // 1. Try package.json
+    try {
+        const packageJson = await fs.readFile(joinPath(projectRoot, 'package.json'));
+        const parsed = JSON.parse(packageJson);
+        if (parsed.name && typeof parsed.name === 'string') {
+            // Strip npm scope (e.g., @org/name → name)
+            const name = parsed.name.replace(/^@[^/]+\//, '');
+            if (name)
+                return toKebabCase(name);
+        }
+    }
+    catch {
+        // package.json not found or unparseable
+    }
+    // 2. Try Cargo.toml
+    try {
+        const cargoToml = await fs.readFile(joinPath(projectRoot, 'Cargo.toml'));
+        const nameMatch = cargoToml.match(/^\s*name\s*=\s*"([^"]+)"/m);
+        if (nameMatch?.[1]) {
+            return toKebabCase(nameMatch[1]);
+        }
+    }
+    catch {
+        // Cargo.toml not found
+    }
+    // 3. Fallback: directory basename
+    const dirName = baseName(projectRoot.replace(/[/\\]$/, ''));
+    return toKebabCase(dirName || 'my-project');
+}
+function toKebabCase(name) {
+    return name
+        .replace(/[^a-zA-Z0-9-]/g, '-')
+        .replace(/([a-z])([A-Z])/g, '$1-$2')
+        .replace(/-+/g, '-')
+        .replace(/^-|-$/g, '')
+        .toLowerCase() || 'my-project';
+}
+// ---------------------------------------------------------------------------
+// Unbound skill detection
+// ---------------------------------------------------------------------------
+/**
+ * Scan workflow paths for .md files without `protocol_id` in frontmatter.
+ * Returns info diagnostics for each unbound skill found.
+ */
+async function detectUnboundSkills(projectRoot, fs) {
+    const diagnostics = [];
+    const workflowDirs = [
+        '.claude/skills',
+        '.cursor/rules',
+        'organon/workflows',
+    ];
+    for (const dir of workflowDirs) {
+        const fullDir = joinPath(projectRoot, dir);
+        if (!await fs.exists(fullDir))
+            continue;
+        let files;
+        try {
+            files = await fs.glob('**/*.md', { cwd: fullDir, ignore: [] });
+        }
+        catch {
+            continue;
+        }
+        for (const file of files) {
+            const fullPath = joinPath(fullDir, file);
+            try {
+                const content = await fs.readFile(fullPath);
+                const { frontmatter } = parseFrontmatter(content);
+                if (!frontmatter?.['protocol_id']) {
+                    diagnostics.push({
+                        severity: 'info',
+                        code: 'INIT_SKILL_NO_BINDING',
+                        message: `Skill '${joinPath(dir, file)}' has no protocol_id binding — consider adding protocol_id and protocol_file to its frontmatter`,
+                        file: joinPath(dir, file),
+                    });
+                }
+            }
+            catch {
+                // Skip files we can't read
+            }
+        }
+    }
+    return diagnostics;
+}
 // ---------------------------------------------------------------------------
 // Main
 // ---------------------------------------------------------------------------
@@ -16,13 +107,17 @@ export async function init(options) {
     const files = new Map();
     const skipped = [];
     const diagnostics = [];
-    // 1. Generate organon scaffold files
+    // Detect project name
+    const projectName = options.projectName ?? await detectProjectName(projectRoot, fs);
+    // 1. Generate organon scaffold files (with parameterized templates)
     const organonFiles = [
         ['organon.config.json', CONFIG_TEMPLATE],
         ['CLAUDE.md', CLAUDE_MD_TEMPLATE],
-        ['organon/ETHOS.md', ETHOS_TEMPLATE],
-        ['organon/PHILOSOPHY.md', PHILOSOPHY_TEMPLATE],
+        ['organon/ETHOS.md', ethosTemplate(projectName)],
+        ['organon/PHILOSOPHY.md', philosophyTemplate(projectName)],
         ['organon/README.md', README_TEMPLATE],
+        ['organon/PRIMER.md', PRIMER_TEMPLATE],
+        ['organon/methodology-reference.md', METHODOLOGY_REFERENCE_TEMPLATE],
         ['organon/protocols/PROTOCOLS.md', PROTOCOLS_TEMPLATE],
         ['organon/observations/README.md', OBSERVATIONS_README_TEMPLATE],
     ];
@@ -82,7 +177,10 @@ export async function init(options) {
             }
         }
     }
-    // 3. Summary diagnostic
+    // 3. Detect pre-existing unbound skills (A3)
+    const unboundDiags = await detectUnboundSkills(projectRoot, fs);
+    diagnostics.push(...unboundDiags);
+    // 4. Summary diagnostic
     if (files.size === 0 && skipped.length > 0) {
         diagnostics.push({
             severity: 'info',

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+{"version":3,"file":"init.js","sourceRoot":"","sources":["../../src/core/init.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAGH,OAAO,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,aAAa,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAC;AAC3D,OAAO,EACL,iBAAiB,EACjB,aAAa,EACb,kBAAkB,EAClB,eAAe,EACf,kBAAkB,EAClB,kBAAkB,EAClB,4BAA4B,EAC5B,eAAe,EACf,8BAA8B,EAC9B,eAAe,GAChB,MAAM,uBAAuB,CAAC;AAwB/B,8EAA8E;AAC9E,yBAAyB;AACzB,8EAA8E;AAE9E;;GAEG;AACH,MAAM,CAAC,KAAK,UAAU,iBAAiB,CACrC,WAAmB,EACnB,EAAc;IAEd,sBAAsB;IACtB,IAAI,CAAC;QACH,MAAM,WAAW,GAAG,MAAM,EAAE,CAAC,QAAQ,CAAC,QAAQ,CAAC,WAAW,EAAE,cAAc,CAAC,CAAC,CAAC;QAC7E,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,CAAC;QACvC,IAAI,MAAM,CAAC,IAAI,IAAI,OAAO,MAAM,CAAC,IAAI,KAAK,QAAQ,EAAE,CAAC;YACnD,2CAA2C;YAC3C,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,WAAW,EAAE,EAAE,CAAC,CAAC;YAClD,IAAI,IAAI;gBAAE,OAAO,WAAW,CAAC,IAAI,CAAC,CAAC;QACrC,CAAC;IACH,CAAC;IAAC,MAAM,CAAC;QACP,wCAAwC;IAC1C,CAAC;IAED,oBAAoB;IACpB,IAAI,CAAC;QACH,MAAM,SAAS,GAAG,MAAM,EAAE,CAAC,QAAQ,CAAC,QAAQ,CAAC,WAAW,EAAE,YAAY,CAAC,CAAC,CAAC;QACzE,MAAM,SAAS,GAAG,SAAS,CAAC,KAAK,CAAC,2BAA2B,CAAC,CAAC;QAC/D,IAAI,SAAS,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YACnB,OAAO,WAAW,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC;QACnC,CAAC;IACH,CAAC;IAAC,MAAM,CAAC;QACP,uBAAuB;IACzB,CAAC;IAED,kCAAkC;IAClC,MAAM,OAAO,GAAG,QAAQ,CAAC,WAAW,CAAC,OAAO,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC,CAAC;IAC5D,OAAO,WAAW,CAAC,OAAO,IAAI,YAAY,CAAC,CAAC;AAC9C,CAAC;AAED,SAAS,WAAW,CAAC,IAAY;IAC/B,OAAO,IAAI;SACR,OAAO,CAAC,gBAAgB,EAAE,GAAG,CAAC;SAC9B,OAAO,CAAC,iBAAiB,EAAE,OAAO,CAAC;SACnC,OAAO,CAAC,KAAK,EAAE,GAAG,CAAC;SACnB,OAAO,CAAC,QAAQ,EAAE,EAAE,CAAC;SACrB,WAAW,EAAE,IAAI,YAAY,CAAC;AACnC,CAAC;AAED,8EAA8E;AAC9E,0BAA0B;AAC1B,8EAA8E;AAE9E;;;GAGG;AACH,KAAK,UAAU,mBAAmB,CAChC,WAAmB,EACnB,EAAc;IAEd,MAAM,WAAW,GAAwB,EAAE,CAAC;IAE5C,MAAM,YAAY,GAAG;QACnB,gBAAgB;QAChB,eAAe;QACf,mBAAmB;KACpB,CAAC;IAEF,KAAK,MAAM,GAAG,IAAI,YAAY,EAAE,CAAC;QAC/B,MAAM,OAAO,GAAG,QAAQ,CAAC,WAAW,EAAE,GAAG,CAAC,CAAC;QAC3C,IAAI,CAAC,MAAM,EAAE,CAAC,MAAM,CAAC,OAAO,CAAC;YAAE,SAAS;QAExC,IAAI,KAAe,CAAC;QACpB,IAAI,CAAC;YACH,KAAK,GAAG,MAAM,EAAE,CAAC,IAAI,CAAC,SAAS,EAAE,EAAE,GAAG,EAAE,OAAO,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,CAAC;QACjE,CAAC;QAAC,MAAM,CAAC;YACP,SAAS;QACX,CAAC;QAED,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;YACzB,MAAM,QAAQ,GAAG,QAAQ,CAAC,OAAO,EAAE,IAAI,CAAC,CAAC;YACzC,IAAI,CAAC;gBACH,MAAM,OAAO,GAAG,MAAM,EAAE,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC;gBAC5C,MAAM,EAAE,WAAW,EAAE,GAAG,gBAAgB,CAAC,OAAO,CAAC,CAAC;gBAClD,IAAI,CAAC,WAAW,EAAE,CAAC,aAAa,CAAC,EAAE,CAAC;oBAClC,WAAW,CAAC,IAAI,CAAC;wBACf,QAAQ,EAAE,MAAM;wBAChB,IAAI,EAAE,uBAAuB;wBAC7B,OAAO,EAAE,UAAU,QAAQ,CAAC,GAAG,EAAE,IAAI,CAAC,iGAAiG;wBACvI,IAAI,EAAE,QAAQ,CAAC,GAAG,EAAE,IAAI,CAAC;qBAC1B,CAAC,CAAC;gBACL,CAAC;YACH,CAAC;YAAC,MAAM,CAAC;gBACP,2BAA2B;YAC7B,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,WAAW,CAAC;AACrB,CAAC;AAED,8EAA8E;AAC9E,OAAO;AACP,8EAA8E;AAE9E,MAAM,CAAC,KAAK,UAAU,IAAI,CAAC,OAAoB;IAC7C,MAAM,EAAE,WAAW,EAAE,aAAa,EAAE,KAAK,EAAE,EAAE,EAAE,GAAG,OAAO,CAAC;IAE1D,MAAM,KAAK,GAAG,IAAI,GAAG,EAAkB,CAAC;IACxC,MAAM,OAAO,GAAa,EAAE,CAAC;IAC7B,MAAM,WAAW,GAAwB,EAAE,CAAC;IAE5C,sBAAsB;IACtB,MAAM,WAAW,GAAG,OAAO,CAAC,WAAW,IAAI,MAAM,iBAAiB,CAAC,WAAW,EAAE,EAAE,CAAC,CAAC;IAEpF,oEAAoE;IACpE,MAAM,YAAY,GAA4B;QAC5C,CAAC,qBAAqB,EAAE,eAAe,CAAC;QACxC,CAAC,WAAW,EAAE,kBAAkB,CAAC;QACjC,CAAC,kBAAkB,EAAE,aAAa,CAAC,WAAW,CAAC,CAAC;QAChD,CAAC,uBAAuB,EAAE,kBAAkB,CAAC,WAAW,CAAC,CAAC;QAC1D,CAAC,mBAAmB,EAAE,eAAe,CAAC;QACtC,CAAC,mBAAmB,EAAE,eAAe,CAAC;QACtC,CAAC,kCAAkC,EAAE,8BAA8B,CAAC;QACpE,CAAC,gCAAgC,EAAE,kBAAkB,CAAC;QACtD,CAAC,gCAAgC,EAAE,4BAA4B,CAAC;KACjE,CAAC;IAEF,KAAK,MAAM,CAAC,YAAY,EAAE,OAAO,CAAC,IAAI,YAAY,EAAE,CAAC;QACnD,IAAI,CAAC;YACH,MAAM,QAAQ,GAAG,QAAQ,CAAC,WAAW,EAAE,YAAY,CAAC,CAAC;YACrD,MAAM,MAAM,GAAG,MAAM,EAAE,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC;YAEzC,IAAI,MAAM,IAAI,CAAC,KAAK,EAAE,CAAC;gBACrB,OAAO,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC;gBAC3B,WAAW,CAAC,IAAI,CAAC;oBACf,QAAQ,EAAE,MAAM;oBAChB,IAAI,EAAE,kBAAkB;oBACxB,OAAO,EAAE,6BAA6B,YAAY,EAAE;oBACpD,IAAI,EAAE,YAAY;iBACnB,CAAC,CAAC;YACL,CAAC;iBAAM,CAAC;gBACN,KAAK,CAAC,GAAG,CAAC,YAAY,EAAE,OAAO,CAAC,CAAC;YACnC,CAAC;QACH,CAAC;QAAC,OAAO,GAAG,EAAE,CAAC;YACb,WAAW,CAAC,IAAI,CAAC;gBACf,QAAQ,EAAE,OAAO;gBACjB,IAAI,EAAE,kBAAkB;gBACxB,OAAO,EAAE,mBAAmB,YAAY,KAAK,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE;gBAC/F,IAAI,EAAE,YAAY;aACnB,CAAC,CAAC;QACL,CAAC;IACH,CAAC;IAED,yCAAyC;IACzC,IAAI,aAAa,EAAE,CAAC;QAClB,MAAM,cAAc,GAAG,iBAAiB,EAAE,CAAC;QAC3C,KAAK,MAAM,CAAC,EAAE,EAAE,IAAI,EAAE,YAAY,EAAE,OAAO,EAAE,CAAC,IAAI,cAAc,EAAE,CAAC;YACjE,IAAI,CAAC;gBACH,MAAM,QAAQ,GAAG,QAAQ,CAAC,WAAW,EAAE,YAAY,CAAC,CAAC;gBACrD,MAAM,MAAM,GAAG,MAAM,EAAE,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC;gBAEzC,IAAI,MAAM,IAAI,CAAC,KAAK,EAAE,CAAC;oBACrB,OAAO,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC;oBAC3B,WAAW,CAAC,IAAI,CAAC;wBACf,QAAQ,EAAE,MAAM;wBAChB,IAAI,EAAE,mBAAmB;wBACzB,OAAO,EAAE,mCAAmC,YAAY,EAAE;wBAC1D,IAAI,EAAE,YAAY;qBACnB,CAAC,CAAC;gBACL,CAAC;qBAAM,CAAC;oBACN,KAAK,CAAC,GAAG,CAAC,YAAY,EAAE,OAAO,CAAC,CAAC;gBACnC,CAAC;YACH,CAAC;YAAC,OAAO,GAAG,EAAE,CAAC;gBACb,WAAW,CAAC,IAAI,CAAC;oBACf,QAAQ,EAAE,OAAO;oBACjB,IAAI,EAAE,kBAAkB;oBACxB,OAAO,EAA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package/dist/core/init.test.js

@@ -18,12 +18,14 @@ describe('init', () => {
             fs,
         });
         expect(result.success).toBe(true);
-        expect(result.files.size).toBeGreaterThanOrEqual(7);
+        expect(result.files.size).toBeGreaterThanOrEqual(9);
         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/PRIMER.md')).toBe(true);
+        expect(result.files.has('organon/methodology-reference.md')).toBe(true);
         expect(result.files.has('organon/protocols/PROTOCOLS.md')).toBe(true);
         expect(result.files.has('organon/observations/README.md')).toBe(true);
     });
@@ -36,7 +38,7 @@ describe('init', () => {
             fs,
         });
         expect(result.success).toBe(true);
-        expect(result.files.size).toBe(7 + getSkillTemplates().size);
+        expect(result.files.size).toBe(9 + 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);
@@ -83,6 +85,8 @@ describe('init', () => {
             '/project/organon/ETHOS.md': '# ethos',
             '/project/organon/PHILOSOPHY.md': '# phil',
             '/project/organon/README.md': '# readme',
+            '/project/organon/PRIMER.md': '# primer',
+            '/project/organon/methodology-reference.md': '# reference',
             '/project/organon/protocols/PROTOCOLS.md': '# protocols',
             '/project/organon/observations/README.md': '# observations',
         });
@@ -94,7 +98,7 @@ describe('init', () => {
         });
         expect(result.success).toBe(true);
         expect(result.files.size).toBe(0);
-        expect(result.skipped.length).toBe(7);
+        expect(result.skipped.length).toBe(9);
         const codes = result.diagnostics.map((d) => d.code);
         expect(codes).toContain('INIT_ALREADY_INITIALIZED');
     });
@@ -199,5 +203,117 @@ describe('init', () => {
         // Other skills should still be generated
         expect(result.files.has('.claude/skills/quality-review/SKILL.md')).toBe(true);
     });
+    it('infers project name from package.json', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/package.json': JSON.stringify({ name: '@scope/my-awesome-project' }),
+        });
+        const result = await init({
+            projectRoot: '/project',
+            installSkills: false,
+            force: false,
+            fs,
+        });
+        const ethosContent = result.files.get('organon/ETHOS.md');
+        expect(ethosContent).toContain('name: my-awesome-project');
+        expect(ethosContent).toContain('Behavioral constraints for my-awesome-project');
+    });
+    it('infers project name from Cargo.toml when no package.json', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/Cargo.toml': '[package]\nname = "rust-tool"\nversion = "0.1.0"',
+        });
+        const result = await init({
+            projectRoot: '/project',
+            installSkills: false,
+            force: false,
+            fs,
+        });
+        const ethosContent = result.files.get('organon/ETHOS.md');
+        expect(ethosContent).toContain('name: rust-tool');
+    });
+    it('falls back to directory name for project name', async () => {
+        const fs = new MemoryFileSystem();
+        const result = await init({
+            projectRoot: '/repos/cool-project',
+            installSkills: false,
+            force: false,
+            fs,
+        });
+        const ethosContent = result.files.get('organon/ETHOS.md');
+        expect(ethosContent).toContain('name: cool-project');
+    });
+    it('uses explicit projectName override', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/package.json': JSON.stringify({ name: 'pkg-name' }),
+        });
+        const result = await init({
+            projectRoot: '/project',
+            installSkills: false,
+            force: false,
+            fs,
+            projectName: 'custom-name',
+        });
+        const ethosContent = result.files.get('organon/ETHOS.md');
+        expect(ethosContent).toContain('name: custom-name');
+    });
+    it('detects pre-existing unbound skills', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/.claude/skills/my-skill/SKILL.md': `---
+name: my-skill
+---
+
+# My Skill
+
+No protocol_id here.
+`,
+        });
+        const result = await init({
+            projectRoot: '/project',
+            installSkills: false,
+            force: false,
+            fs,
+        });
+        const unboundDiags = result.diagnostics.filter((d) => d.code === 'INIT_SKILL_NO_BINDING');
+        expect(unboundDiags.length).toBe(1);
+        expect(unboundDiags[0].message).toContain('protocol_id');
+    });
+    it('does not flag skills with protocol_id as unbound', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/.claude/skills/bound-skill/SKILL.md': `---
+name: bound-skill
+protocol_id: PROTO-TEST-1
+protocol_file: organon/protocols/PROTOCOLS.md
+tools:
+  - organon-verify
+loads:
+  - organon/ETHOS.md
+---
+
+# Bound Skill
+`,
+        });
+        const result = await init({
+            projectRoot: '/project',
+            installSkills: false,
+            force: false,
+            fs,
+        });
+        const unboundDiags = result.diagnostics.filter((d) => d.code === 'INIT_SKILL_NO_BINDING');
+        expect(unboundDiags.length).toBe(0);
+    });
+    it('generated config has testGlobs and testIgnorePatterns', 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.testGlobs).toBeDefined();
+        expect(config.testGlobs).toContain('**/*.test.ts');
+        expect(config.testIgnorePatterns).toBeDefined();
+    });
 });
 //# sourceMappingURL=init.test.js.map

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

@@ -1 +1 @@
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package/dist/core/invariant-coverage.d.ts.map

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