@organon-methodology/tools 0.3.0

package/dist/core/suggest-tools.js

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+/**
+ * Automation suggestion heuristics.
+ *
+ * Analyzes protocols and suggests which ones should be upgraded
+ * from manual → semi-automated → automated, based on step count,
+ * complexity, frequency indicators, and error-proneness.
+ */
+import { parseFrontmatter } from './frontmatter-parser.js';
+import { joinPath } from './config.js';
+// ---------------------------------------------------------------------------
+// Constants
+// ---------------------------------------------------------------------------
+const STEP_THRESHOLD_AUTOMATED = 5;
+const STEP_THRESHOLD_SEMI = 2;
+// Keywords that indicate error-proneness or frequency
+const ERROR_PRONE_KEYWORDS = [
+    'careful', 'ensure', 'verify', 'must', 'critical',
+    'never', 'always', 'exactly', 'precisely',
+];
+const FREQUENCY_KEYWORDS = [
+    'every', 'each', 'always', 'regularly', 'frequently',
+    'before each', 'after each', 'on every',
+];
+const CROSS_DOMAIN_KEYWORDS = [
+    'across', 'multiple', 'all domains', 'cross-cutting',
+    'throughout', 'every domain',
+];
+// ---------------------------------------------------------------------------
+// Main
+// ---------------------------------------------------------------------------
+export async function suggestTools(options) {
+    const { projectRoot, config, fs } = options;
+    const errors = [];
+    const warnings = [];
+    const suggestions = [];
+    // Discover protocol files
+    const organonFiles = await discoverOrganonFiles(projectRoot, config, fs);
+    for (const file of organonFiles) {
+        const absPath = joinPath(projectRoot, file);
+        let content;
+        try {
+            content = await fs.readFile(absPath);
+        }
+        catch {
+            continue;
+        }
+        const { frontmatter, body } = parseFrontmatter(content);
+        if (frontmatter?.type !== 'procedures' || !frontmatter.protocols)
+            continue;
+        for (const proto of frontmatter.protocols) {
+            const suggestedTier = suggestTier(proto.steps, proto.automation_tier, body);
+            if (suggestedTier && suggestedTier !== proto.automation_tier) {
+                const reason = buildReason(proto.steps, proto.automation_tier, suggestedTier, body);
+                suggestions.push({
+                    protocolId: proto.id,
+                    protocolFile: file,
+                    currentTier: proto.automation_tier,
+                    suggestedTier,
+                    reason,
+                    steps: proto.steps,
+                    complexity: proto.complexity,
+                });
+            }
+        }
+    }
+    return {
+        success: errors.length === 0,
+        suggestions,
+        errors,
+        warnings,
+    };
+}
+// ---------------------------------------------------------------------------
+// Suggestion logic
+// ---------------------------------------------------------------------------
+function suggestTier(steps, currentTier, body) {
+    const lower = body.toLowerCase();
+    const errorProneScore = ERROR_PRONE_KEYWORDS.reduce((count, kw) => count + (lower.includes(kw) ? 1 : 0), 0);
+    const frequencyScore = FREQUENCY_KEYWORDS.reduce((count, kw) => count + (lower.includes(kw) ? 1 : 0), 0);
+    const crossDomainScore = CROSS_DOMAIN_KEYWORDS.reduce((count, kw) => count + (lower.includes(kw) ? 1 : 0), 0);
+    const totalScore = errorProneScore + frequencyScore + crossDomainScore;
+    // Suggest upgrade based on step count + heuristic score
+    if (currentTier === 'manual') {
+        if (steps >= STEP_THRESHOLD_AUTOMATED || totalScore >= 4) {
+            return 'automated';
+        }
+        if (steps >= STEP_THRESHOLD_SEMI || totalScore >= 2) {
+            return 'semi-automated';
+        }
+    }
+    if (currentTier === 'semi-automated') {
+        if (steps >= STEP_THRESHOLD_AUTOMATED || totalScore >= 4) {
+            return 'automated';
+        }
+    }
+    return null;
+}
+function buildReason(steps, currentTier, suggestedTier, body) {
+    const reasons = [];
+    const lower = body.toLowerCase();
+    if (steps >= STEP_THRESHOLD_AUTOMATED) {
+        reasons.push(`${steps} steps (threshold: ${STEP_THRESHOLD_AUTOMATED})`);
+    }
+    else if (steps >= STEP_THRESHOLD_SEMI) {
+        reasons.push(`${steps} steps`);
+    }
+    const hasErrorProne = ERROR_PRONE_KEYWORDS.some((kw) => lower.includes(kw));
+    if (hasErrorProne)
+        reasons.push('error-prone language detected');
+    const hasFrequency = FREQUENCY_KEYWORDS.some((kw) => lower.includes(kw));
+    if (hasFrequency)
+        reasons.push('frequent execution indicated');
+    const hasCrossDomain = CROSS_DOMAIN_KEYWORDS.some((kw) => lower.includes(kw));
+    if (hasCrossDomain)
+        reasons.push('cross-domain scope');
+    return reasons.length > 0
+        ? `Upgrade ${currentTier} → ${suggestedTier}: ${reasons.join(', ')}`
+        : `Consider upgrading from ${currentTier} to ${suggestedTier}`;
+}
+// ---------------------------------------------------------------------------
+// Helpers
+// ---------------------------------------------------------------------------
+async function discoverOrganonFiles(projectRoot, config, fs) {
+    const allFiles = new Set();
+    for (const organonPath of config.organonPaths) {
+        for (const pattern of config.organonGlobs) {
+            const fullPattern = organonPath === '.' ? pattern : `${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=suggest-tools.js.map

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package/dist/core/suggest-tools.test.d.ts

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+export {};
+//# sourceMappingURL=suggest-tools.test.d.ts.map

package/dist/core/suggest-tools.test.d.ts.map

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

package/dist/core/suggest-tools.test.js

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+import { describe, it, expect } from 'vitest';
+import { suggestTools } from './suggest-tools.js';
+import { MemoryFileSystem } from './test-helpers.js';
+function makeConfig(projectRoot) {
+    return {
+        projectRoot,
+        organonPaths: ['.'],
+        organonGlobs: ['**/PROTOCOLS.md'],
+        ignorePatterns: [],
+        workflowPaths: {},
+        freshnessThresholdHours: 24,
+    };
+}
+describe('suggestTools', () => {
+    it('suggests upgrading manual protocol with many steps', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/PROTOCOLS.md': `---
+type: procedures
+scope: methodology
+name: test
+version: "1.0"
+summary: Test
+token_estimate: 500
+protocols_count: 1
+protocols:
+  - id: PROTO-BIG-1
+    name: Big Manual Protocol
+    steps: 8
+    automation_tier: manual
+    complexity: high
+---
+
+## Steps
+
+You must always ensure every step is done carefully.
+This is critical and must never be skipped.
+Before each deployment, verify all checks pass.
+
+1. Step one
+2. Step two
+3. Step three
+4. Step four
+5. Step five
+6. Step six
+7. Step seven
+8. Step eight`,
+        });
+        const config = makeConfig('/project');
+        const result = await suggestTools({ projectRoot: '/project', config, fs });
+        expect(result.suggestions.length).toBeGreaterThanOrEqual(1);
+        expect(result.suggestions[0].suggestedTier).toBe('automated');
+        expect(result.suggestions[0].currentTier).toBe('manual');
+    });
+    it('does not suggest changes for already automated protocols', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/PROTOCOLS.md': `---
+type: procedures
+scope: methodology
+name: test
+version: "1.0"
+summary: Test
+token_estimate: 300
+protocols_count: 1
+protocols:
+  - id: PROTO-AUTO-1
+    name: Already Automated
+    steps: 6
+    automation_tier: automated
+    workflow: my-workflow
+    complexity: high
+---
+
+## Steps
+1. Step one`,
+        });
+        const config = makeConfig('/project');
+        const result = await suggestTools({ projectRoot: '/project', config, fs });
+        expect(result.suggestions.length).toBe(0);
+    });
+    it('suggests semi-automated for small manual protocols with error-prone language', async () => {
+        const fs = new MemoryFileSystem({
+            '/project/PROTOCOLS.md': `---
+type: procedures
+scope: methodology
+name: test
+version: "1.0"
+summary: Test
+token_estimate: 300
+protocols_count: 1
+protocols:
+  - id: PROTO-SMALL-1
+    name: Small Protocol
+    steps: 3
+    automation_tier: manual
+    complexity: low
+---
+
+## Steps
+
+You must carefully ensure the output is precisely correct.
+Always verify before proceeding.
+
+1. Step one
+2. Step two
+3. Step three`,
+        });
+        const config = makeConfig('/project');
+        const result = await suggestTools({ projectRoot: '/project', config, fs });
+        expect(result.suggestions.length).toBeGreaterThanOrEqual(1);
+        const suggestion = result.suggestions[0];
+        expect(suggestion.currentTier).toBe('manual');
+        expect(['semi-automated', 'automated']).toContain(suggestion.suggestedTier);
+    });
+    it('returns empty suggestions for projects without protocols', async () => {
+        const fs = new MemoryFileSystem();
+        const config = makeConfig('/project');
+        const result = await suggestTools({ projectRoot: '/project', config, fs });
+        expect(result.suggestions).toHaveLength(0);
+        expect(result.success).toBe(true);
+    });
+});
+//# sourceMappingURL=suggest-tools.test.js.map

package/dist/core/suggest-tools.test.js.map

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

@@ -0,0 +1,63 @@
+/**
+ * In-memory FileSystem for testing core functions.
+ */
+import type { FileSystem, FileStat } from './types.js';
+export declare class MemoryFileSystem implements FileSystem {
+    private files;
+    private throwPaths;
+    private throwReadPaths;
+    constructor(files?: Record<string, string>);
+    addFile(path: string, content: string, mtime?: Date): void;
+    /** Make exists() and readFile() throw for any path containing this substring. */
+    throwOn(pathSubstring: string): void;
+    /** Make only readFile() throw for any path containing this substring (exists() still works). */
+    throwOnRead(pathSubstring: string): void;
+    private checkThrow;
+    private checkThrowRead;
+    readFile(path: string): Promise<string>;
+    readDir(dirPath: string): Promise<string[]>;
+    exists(path: string): Promise<boolean>;
+    glob(pattern: string, options?: {
+        cwd: string;
+        ignore?: string[];
+    }): Promise<string[]>;
+    stat(path: string): Promise<FileStat>;
+}
+/**
+ * Create a minimal ETHOS.md file content for testing.
+ */
+export declare function makeEthos(opts?: {
+    name?: string;
+    scope?: string;
+    invariants?: number;
+    principles?: number;
+    heuristics?: number;
+    extra?: Record<string, unknown>;
+}): string;
+/**
+ * Create a minimal PHILOSOPHY.md for testing.
+ */
+export declare function makePhilosophy(opts?: {
+    name?: string;
+    decisions?: number;
+}): string;
+/**
+ * Create a minimal README.md for testing.
+ */
+export declare function makeReadme(opts?: {
+    name?: string;
+    scope?: string;
+}): string;
+/**
+ * Create a minimal workflow file for testing.
+ */
+export declare function makeWorkflow(opts?: {
+    name?: string;
+    protocolId?: string;
+    protocolFile?: string;
+    tools?: string[];
+    loads?: string[];
+    includeRecovery?: boolean;
+    steps?: number;
+}): string;
+//# sourceMappingURL=test-helpers.d.ts.map

package/dist/core/test-helpers.d.ts.map

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package/dist/core/test-helpers.js

@@ -0,0 +1,265 @@
+/**
+ * In-memory FileSystem for testing core functions.
+ */
+export class MemoryFileSystem {
+    files = new Map();
+    throwPaths = new Set();
+    throwReadPaths = new Set();
+    constructor(files) {
+        if (files) {
+            for (const [path, content] of Object.entries(files)) {
+                this.addFile(path, content);
+            }
+        }
+    }
+    addFile(path, content, mtime) {
+        this.files.set(normalize(path), {
+            content,
+            mtime: mtime ?? new Date(),
+        });
+    }
+    /** Make exists() and readFile() throw for any path containing this substring. */
+    throwOn(pathSubstring) {
+        this.throwPaths.add(pathSubstring);
+    }
+    /** Make only readFile() throw for any path containing this substring (exists() still works). */
+    throwOnRead(pathSubstring) {
+        this.throwReadPaths.add(pathSubstring);
+    }
+    checkThrow(path) {
+        for (const sub of this.throwPaths) {
+            if (path.includes(sub)) {
+                throw new Error(`EPERM: permission denied, '${path}'`);
+            }
+        }
+    }
+    checkThrowRead(path) {
+        for (const sub of this.throwReadPaths) {
+            if (path.includes(sub)) {
+                throw new Error(`EPERM: permission denied, '${path}'`);
+            }
+        }
+    }
+    async readFile(path) {
+        this.checkThrow(path);
+        this.checkThrowRead(path);
+        const file = this.files.get(normalize(path));
+        if (!file)
+            throw new Error(`ENOENT: ${path}`);
+        return file.content;
+    }
+    async readDir(dirPath) {
+        const dir = normalize(dirPath);
+        const entries = new Set();
+        for (const key of this.files.keys()) {
+            if (key.startsWith(dir + '/')) {
+                const rest = key.slice(dir.length + 1);
+                const firstSegment = rest.split('/')[0];
+                entries.add(firstSegment);
+            }
+        }
+        return [...entries];
+    }
+    async exists(path) {
+        this.checkThrow(path);
+        const norm = normalize(path);
+        // Check exact file match
+        if (this.files.has(norm))
+            return true;
+        // Check if it's a directory (any file starts with this path)
+        for (const key of this.files.keys()) {
+            if (key.startsWith(norm + '/'))
+                return true;
+        }
+        return false;
+    }
+    async glob(pattern, options) {
+        const cwd = options?.cwd ? normalize(options.cwd) : '';
+        const ignorePatterns = options?.ignore ?? [];
+        const results = [];
+        for (const key of this.files.keys()) {
+            // Files in cwd
+            const relative = cwd ? (key.startsWith(cwd + '/') ? key.slice(cwd.length + 1) : null) : key;
+            if (relative === null)
+                continue;
+            // Simple glob matching
+            if (matchGlob(relative, pattern)) {
+                // Check ignore patterns
+                const ignored = ignorePatterns.some((ip) => matchGlob(relative, ip));
+                if (!ignored) {
+                    results.push(relative);
+                }
+            }
+        }
+        return results.sort();
+    }
+    async stat(path) {
+        const file = this.files.get(normalize(path));
+        if (!file)
+            throw new Error(`ENOENT: ${path}`);
+        return { mtime: file.mtime, size: file.content.length };
+    }
+}
+function normalize(p) {
+    return p.replace(/\\/g, '/').replace(/\/+/g, '/').replace(/\/$/, '');
+}
+/**
+ * Simple glob matcher supporting:
+ *   **  = any path segments
+ *   *   = any characters except /
+ */
+function matchGlob(path, pattern) {
+    // Convert glob to regex
+    let regexStr = pattern
+        .replace(/\./g, '\\.')
+        .replace(/\*\*\//g, '§§/') // temp placeholder for **/
+        .replace(/\*\*/g, '§§') // temp placeholder for bare **
+        .replace(/\*/g, '[^/]*') // * matches anything except /
+        .replace(/§§\//g, '(.*/)?') // **/ matches zero or more path segments
+        .replace(/§§/g, '.*'); // ** matches anything including /
+    const regex = new RegExp(`^${regexStr}$`);
+    return regex.test(path);
+}
+/**
+ * Create a minimal ETHOS.md file content for testing.
+ */
+export function makeEthos(opts) {
+    const { name = 'test-ethos', scope = 'domain', invariants = 3, principles = 2, heuristics = 2, extra = {}, } = opts ?? {};
+    const extraEntries = Object.entries(extra)
+        .map(([k, v]) => `${k}: ${typeof v === 'object' ? JSON.stringify(v) : v}`);
+    const extraFields = extraEntries.length > 0 ? extraEntries.join('\n') + '\n' : '';
+    const invLines = Array.from({ length: invariants }, (_, i) => `${i + 1}. **Rule ${i + 1}.** Description of rule ${i + 1}.`).join('\n');
+    const priLines = Array.from({ length: principles }, (_, i) => `${i + 1}. **Principle ${i + 1}.** Description of principle ${i + 1}.`).join('\n');
+    const heuristicRows = Array.from({ length: heuristics }, (_, i) => `| Situation ${i + 1} | Action ${i + 1} |`).join('\n');
+    const tokenEstimate = Math.ceil((`---\ntype: constraints\nscope: ${scope}\nname: ${name}\nversion: "1.0"\nsummary: Test ethos\ntoken_estimate: 500\ninvariants_count: ${invariants}\nprinciples_count: ${principles}\nheuristics_count: ${heuristics}\n${extraFields}\n---\n\n# ${name}\n\n## Identity\n\n### What ${name} IS\n- A test\n\n### What ${name} IS NOT\n- Not production\n\n## Invariants\n\n${invLines}\n\n## Principles (Prioritized)\n\n${priLines}\n\n## Decision Heuristics\n\n| Situation | Action |\n|-----------|--------|\n${heuristicRows}\n`).length / 4);
+    return `---
+type: constraints
+scope: ${scope}
+name: ${name}
+version: "1.0"
+summary: Test ethos
+token_estimate: ${tokenEstimate}
+invariants_count: ${invariants}
+principles_count: ${principles}
+heuristics_count: ${heuristics}
+${extraFields}---
+
+# ${name}
+
+## Identity
+
+### What ${name} IS
+- A test
+
+### What ${name} IS NOT
+- Not production
+
+## Invariants
+
+${invLines}
+
+## Principles (Prioritized)
+
+${priLines}
+
+## Decision Heuristics
+
+| Situation | Action |
+|-----------|--------|
+${heuristicRows}
+`;
+}
+/**
+ * Create a minimal PHILOSOPHY.md for testing.
+ */
+export function makePhilosophy(opts) {
+    const { name = 'test-philosophy', decisions = 2 } = opts ?? {};
+    const decisionLines = Array.from({ length: decisions }, (_, i) => `### ${i + 1}. Decision ${i + 1}\nDescription.\n**Rationale:** Because.`).join('\n\n');
+    return `---
+type: rationale
+scope: domain
+name: ${name}
+version: "1.0"
+summary: Test philosophy
+token_estimate: 400
+decision_count: ${decisions}
+---
+
+# ${name}
+
+## The Problem
+
+Test problem.
+
+## The Bet
+
+Test bet.
+
+## Design Decisions
+
+${decisionLines}
+
+## Trade-offs
+
+| Decision | Benefit | Cost |
+|----------|---------|------|
+| Choice 1 | Gain 1 | Cost 1 |
+`;
+}
+/**
+ * Create a minimal README.md for testing.
+ */
+export function makeReadme(opts) {
+    const { name = 'test-readme', scope = 'domain' } = opts ?? {};
+    return `---
+type: navigation
+scope: ${scope}
+name: ${name}
+version: "1.0"
+summary: Test navigation
+token_estimate: 100
+---
+
+# ${name}
+
+- [ETHOS.md](ETHOS.md)
+- [PHILOSOPHY.md](PHILOSOPHY.md)
+`;
+}
+/**
+ * Create a minimal workflow file for testing.
+ */
+export function makeWorkflow(opts) {
+    const { name = 'test-workflow', protocolId = 'PROTO-TEST-1', protocolFile = 'PROTOCOLS.md', tools = ['tool:verify'], loads = ['/ETHOS.md'], includeRecovery = true, steps = 3, } = opts ?? {};
+    const toolsYaml = tools.map((t) => `  - ${t}`).join('\n');
+    const loadsYaml = loads.map((l) => `  - ${l}`).join('\n');
+    const stepLines = Array.from({ length: steps }, (_, i) => `${i + 1}. **Step ${i + 1}.** Run \`${tools[0] ?? 'tool:action'}\` to do thing ${i + 1}.`).join('\n\n');
+    const recoverySection = includeRecovery
+        ? `\n## Error Recovery\n\n| Failure | Recovery Action |\n|---------|------------------|\n| Tool fails | Re-run after fixing the issue |\n`
+        : '';
+    return `---
+name: ${name}
+protocol_id: ${protocolId}
+protocol_file: ${protocolFile}
+tools:
+${toolsYaml}
+loads:
+${loadsYaml}
+---
+
+# Workflow: ${name}
+
+## Context Loading
+
+1. Load product organons
+
+## Steps
+
+${stepLines}
+
+## Verification
+
+Run verification tools.
+${recoverySection}`;
+}
+//# sourceMappingURL=test-helpers.js.map

package/dist/core/test-helpers.js.map

@@ -0,0 +1 @@
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