@organon-methodology/tools 0.3.0

package/dist/cli/commands/validate.js

@@ -0,0 +1,89 @@
+/**
+ * organon validate — Validate organon frontmatter (4-stage validation).
+ */
+import chalk from 'chalk';
+import { resolveConfig } from '../../core/config.js';
+import { validateFrontmatter } from '../../core/validate-frontmatter.js';
+import { NodeFileSystem } from '../../core/node-fs.js';
+export const validateCommand = {
+    command: 'validate [files..]',
+    describe: 'Validate organon frontmatter (schema, references, truthfulness, consistency)',
+    builder: (yargs) => {
+        return yargs
+            .positional('files', {
+            describe: 'Specific files to validate (validates all if omitted)',
+            type: 'string',
+            array: true,
+        })
+            .option('project-root', {
+            describe: 'Project root directory',
+            type: 'string',
+            default: process.cwd(),
+        })
+            .option('config', {
+            describe: 'Path to organon.config.json',
+            type: 'string',
+        })
+            .option('stages', {
+            describe: 'Validation stages to run (1=schema, 2=references, 3=truthfulness, 4=consistency)',
+            type: 'array',
+            coerce: (arr) => arr.map(Number),
+        })
+            .example('$0 validate', 'Validate all organon files')
+            .example('$0 validate book-llms/ETHOS.md', 'Validate a specific file')
+            .example('$0 validate --stages 1 3', 'Run only schema and truthfulness checks');
+    },
+    handler: async (args) => {
+        const fs = new NodeFileSystem();
+        const config = await resolveConfig(args['project-root'], fs, args.config);
+        const result = await validateFrontmatter({
+            projectRoot: args['project-root'],
+            config,
+            fs,
+            files: args.files,
+            stages: args.stages,
+        });
+        // Output results
+        console.log(chalk.blue('Organon Validate'));
+        console.log();
+        console.log(`Files checked: ${result.filesChecked}`);
+        for (const fileResult of result.results) {
+            if (fileResult.valid && fileResult.warnings.length === 0) {
+                console.log(chalk.green(`  ✓ ${fileResult.file}`));
+            }
+            else if (fileResult.valid) {
+                console.log(chalk.yellow(`  ⚠ ${fileResult.file} (${fileResult.warnings.length} warnings)`));
+                for (const w of fileResult.warnings) {
+                    printDiagnostic(w);
+                }
+            }
+            else {
+                console.log(chalk.red(`  ✗ ${fileResult.file} (${fileResult.errors.length} errors)`));
+                for (const e of fileResult.errors) {
+                    printDiagnostic(e);
+                }
+                for (const w of fileResult.warnings) {
+                    printDiagnostic(w);
+                }
+            }
+        }
+        console.log();
+        if (result.success) {
+            console.log(chalk.green(`✓ All ${result.filesChecked} files passed validation`));
+        }
+        else {
+            console.log(chalk.red(`✗ ${result.filesWithErrors} file(s) failed validation`));
+            process.exit(1);
+        }
+    },
+};
+function printDiagnostic(d) {
+    const prefix = d.severity === 'error' ? chalk.red('    ✗') :
+        d.severity === 'warning' ? chalk.yellow('    ⚠') :
+            chalk.dim('    ℹ');
+    console.log(`${prefix} [${d.code}] ${d.message}`);
+    if (d.suggestion) {
+        console.log(chalk.dim(`      → ${d.suggestion}`));
+    }
+}
+//# sourceMappingURL=validate.js.map

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@@ -0,0 +1 @@
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package/dist/cli/commands/verify.d.ts

@@ -0,0 +1,12 @@
+/**
+ * organon verify — Run verification gates.
+ */
+import type { CommandModule } from 'yargs';
+interface VerifyArgs {
+    'project-root': string;
+    config?: string;
+    gate?: string[];
+}
+export declare const verifyCommand: CommandModule<{}, VerifyArgs>;
+export {};
+//# sourceMappingURL=verify.d.ts.map

package/dist/cli/commands/verify.d.ts.map

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package/dist/cli/commands/verify.js

@@ -0,0 +1,67 @@
+/**
+ * organon verify — Run verification gates.
+ */
+import chalk from 'chalk';
+import { resolveConfig } from '../../core/config.js';
+import { verify } from '../../core/verify.js';
+import { NodeFileSystem } from '../../core/node-fs.js';
+export const verifyCommand = {
+    command: 'verify',
+    describe: 'Run verification gates (frontmatter, triplets, freshness)',
+    builder: (yargs) => {
+        return yargs
+            .option('project-root', {
+            describe: 'Project root directory',
+            type: 'string',
+            default: process.cwd(),
+        })
+            .option('config', {
+            describe: 'Path to organon.config.json',
+            type: 'string',
+        })
+            .option('gate', {
+            describe: 'Run specific gate(s)',
+            type: 'array',
+            string: true,
+        })
+            .example('$0 verify', 'Run all verification gates')
+            .example('$0 verify --gate frontmatter', 'Run only frontmatter gate')
+            .example('$0 verify --gate frontmatter triplets', 'Run specific gates');
+    },
+    handler: async (args) => {
+        const fs = new NodeFileSystem();
+        const config = await resolveConfig(args['project-root'], fs, args.config);
+        const result = await verify({
+            projectRoot: args['project-root'],
+            config,
+            fs,
+            gates: args.gate,
+        });
+        console.log(chalk.blue('Organon Verify'));
+        console.log();
+        for (const gate of result.gates) {
+            const icon = gate.passed ? chalk.green('✓') : chalk.red('✗');
+            console.log(`  ${icon} ${gate.gate}`);
+            for (const e of gate.errors) {
+                const filePrefix = e.file ? `${e.file}: ` : '';
+                console.log(chalk.red(`    ✗ [${e.code}] ${filePrefix}${e.message}`));
+                if (e.suggestion)
+                    console.log(chalk.dim(`      → ${e.suggestion}`));
+            }
+            for (const w of gate.warnings) {
+                const filePrefix = w.file ? `${w.file}: ` : '';
+                console.log(chalk.yellow(`    ⚠ [${w.code}] ${filePrefix}${w.message}`));
+            }
+        }
+        console.log();
+        if (result.success) {
+            console.log(chalk.green(`✓ All ${result.gates.length} gate(s) passed`));
+        }
+        else {
+            const failed = result.gates.filter((g) => !g.passed).length;
+            console.log(chalk.red(`✗ ${failed} gate(s) failed`));
+            process.exit(1);
+        }
+    },
+};
+//# sourceMappingURL=verify.js.map

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package/dist/cli/index.d.ts

@@ -0,0 +1,19 @@
+#!/usr/bin/env node
+/**
+ * Organon CLI — Tools for the Organon Methodology.
+ *
+ * Commands:
+ *   init      — Bootstrap a new project with Organon structure
+ *   upgrade   — Detect version drift and upgrade project
+ *   validate  — Validate organon frontmatter
+ *   generate  — Auto-generate frontmatter from content
+ *   query     — Query organons by metadata
+ *   health    — Health dashboard
+ *   find      — Cross-domain discovery
+ *   verify    — Run verification gates
+ *   coverage       — Invariant coverage analysis
+ *   generate-tests — Generate test scaffolds for uncovered invariants
+ *   mcp            — Start MCP server
+ */
+export {};
+//# sourceMappingURL=index.d.ts.map

package/dist/cli/index.d.ts.map

@@ -0,0 +1 @@
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package/dist/cli/index.js

@@ -0,0 +1,59 @@
+#!/usr/bin/env node
+/**
+ * Organon CLI — Tools for the Organon Methodology.
+ *
+ * Commands:
+ *   init      — Bootstrap a new project with Organon structure
+ *   upgrade   — Detect version drift and upgrade project
+ *   validate  — Validate organon frontmatter
+ *   generate  — Auto-generate frontmatter from content
+ *   query     — Query organons by metadata
+ *   health    — Health dashboard
+ *   find      — Cross-domain discovery
+ *   verify    — Run verification gates
+ *   coverage       — Invariant coverage analysis
+ *   generate-tests — Generate test scaffolds for uncovered invariants
+ *   mcp            — Start MCP server
+ */
+import yargs from 'yargs';
+import { hideBin } from 'yargs/helpers';
+import chalk from 'chalk';
+import { initCommand } from './commands/init.js';
+import { upgradeCommand } from './commands/upgrade.js';
+import { validateCommand } from './commands/validate.js';
+import { generateCommand } from './commands/generate.js';
+import { queryCommand } from './commands/query.js';
+import { healthCommand } from './commands/health.js';
+import { findCommand } from './commands/find.js';
+import { verifyCommand } from './commands/verify.js';
+import { coverageCommand } from './commands/coverage.js';
+import { generateTestsCommand } from './commands/generate-tests.js';
+import { mcpCommand } from './commands/mcp.js';
+async function main() {
+    await yargs(hideBin(process.argv))
+        .scriptName('organon')
+        .usage('$0 <command> [options]')
+        .command(initCommand)
+        .command(upgradeCommand)
+        .command(validateCommand)
+        .command(generateCommand)
+        .command(queryCommand)
+        .command(healthCommand)
+        .command(findCommand)
+        .command(verifyCommand)
+        .command(coverageCommand)
+        .command(generateTestsCommand)
+        .command(mcpCommand)
+        .demandCommand(1, chalk.red('Please specify a command'))
+        .help()
+        .alias('h', 'help')
+        .version()
+        .alias('v', 'version')
+        .strict()
+        .parse();
+}
+main().catch((error) => {
+    console.error(chalk.red('Error:'), error.message);
+    process.exit(1);
+});
+//# sourceMappingURL=index.js.map

package/dist/cli/index.js.map

@@ -0,0 +1 @@
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package/dist/core/add-protocols-array.d.ts

@@ -0,0 +1,17 @@
+/**
+ * Protocol parsing utility.
+ *
+ * Extracts protocol metadata from PROTOCOL.md / PROTOCOLS.md content
+ * by analyzing ## headings, numbered steps, automation tier declarations,
+ * and workflow bindings.
+ */
+import type { ProtocolEntry } from './types.js';
+/**
+ * Parse protocol entries from markdown content.
+ * Looks for patterns like:
+ *   ### PROTO-XXX-N: Protocol Name
+ *   or ## Protocol: Name
+ *   followed by steps, automation tier, etc.
+ */
+export declare function parseProtocols(content: string): ProtocolEntry[];
+//# sourceMappingURL=add-protocols-array.d.ts.map

package/dist/core/add-protocols-array.d.ts.map

@@ -0,0 +1 @@
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package/dist/core/add-protocols-array.js

@@ -0,0 +1,95 @@
+/**
+ * Protocol parsing utility.
+ *
+ * Extracts protocol metadata from PROTOCOL.md / PROTOCOLS.md content
+ * by analyzing ## headings, numbered steps, automation tier declarations,
+ * and workflow bindings.
+ */
+/**
+ * Parse protocol entries from markdown content.
+ * Looks for patterns like:
+ *   ### PROTO-XXX-N: Protocol Name
+ *   or ## Protocol: Name
+ *   followed by steps, automation tier, etc.
+ */
+export function parseProtocols(content) {
+    const protocols = [];
+    // Split by protocol headers (### PROTO-XXX-N or ## Protocol N:)
+    const protocolPattern = /^#{2,3}\s+(?:Protocol\s*:?\s*)?(?<id>PROTO-[\w-]+(?:-\d+)?)\s*[:\-–—]\s*(?<name>.+)$/gm;
+    let match;
+    const allMatches = [];
+    while ((match = protocolPattern.exec(content)) !== null) {
+        allMatches.push({
+            id: match.groups.id,
+            name: match.groups.name.trim(),
+            startIndex: match.index + match[0].length,
+        });
+    }
+    for (let i = 0; i < allMatches.length; i++) {
+        const current = allMatches[i];
+        const endIndex = i + 1 < allMatches.length
+            ? allMatches[i + 1].startIndex - allMatches[i + 1].id.length - 10
+            : content.length;
+        const section = content.slice(current.startIndex, endIndex);
+        const steps = countSteps(section);
+        const automationTier = detectAutomationTier(section);
+        const workflow = extractWorkflow(section);
+        const tools = extractTools(section);
+        const complexity = inferComplexity(steps, automationTier);
+        protocols.push({
+            id: current.id,
+            name: current.name,
+            steps,
+            automation_tier: automationTier,
+            ...(workflow ? { workflow } : {}),
+            ...(tools.length > 0 ? { tools } : {}),
+            complexity,
+        });
+    }
+    return protocols;
+}
+function countSteps(section) {
+    const lines = section.split('\n');
+    let count = 0;
+    for (const line of lines) {
+        const trimmed = line.trim();
+        // Count numbered steps: "1. ", "2. ", etc.
+        if (/^\d+\.\s/.test(trimmed)) {
+            count++;
+        }
+    }
+    return Math.max(count, 1); // At least 1 step
+}
+function detectAutomationTier(section) {
+    const lower = section.toLowerCase();
+    if (/automation[_\s]?tier\s*:\s*automated/i.test(section))
+        return 'automated';
+    if (/automation[_\s]?tier\s*:\s*semi[_-]?automated/i.test(section))
+        return 'semi-automated';
+    if (/automation[_\s]?tier\s*:\s*manual/i.test(section))
+        return 'manual';
+    // Infer from content
+    if (lower.includes('workflow:') || lower.includes('workflow binding'))
+        return 'automated';
+    if (lower.includes('run the') || lower.includes('execute'))
+        return 'semi-automated';
+    return 'manual';
+}
+function extractWorkflow(section) {
+    const match = section.match(/workflow\s*:\s*(\S+)/i);
+    return match ? match[1] : undefined;
+}
+function extractTools(section) {
+    const match = section.match(/tools?\s*:\s*\[([^\]]+)\]/i);
+    if (!match)
+        return [];
+    return match[1].split(',').map((t) => t.trim().replace(/['"]/g, '')).filter(Boolean);
+}
+function inferComplexity(steps, tier) {
+    if (steps >= 8 || tier === 'automated')
+        return 'high';
+    if (steps >= 4 || tier === 'semi-automated')
+        return 'medium';
+    return 'low';
+}
+//# sourceMappingURL=add-protocols-array.js.map

package/dist/core/add-protocols-array.js.map

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package/dist/core/add-protocols-array.test.d.ts

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

package/dist/core/add-protocols-array.test.d.ts.map

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

package/dist/core/add-protocols-array.test.js

@@ -0,0 +1,86 @@
+import { describe, it, expect } from 'vitest';
+import { parseProtocols } from './add-protocols-array.js';
+describe('parseProtocols', () => {
+    it('parses protocol entries from markdown', () => {
+        const content = `
+### PROTO-RFC-1: RFC Implementation
+
+1. Create RFC document
+2. Write impact section
+3. Get review
+4. Implement
+5. Update organon
+6. Merge
+
+Automation tier: automated
+Workflow: implement-rfc
+Tools: [rfc:context, rfc:verify]
+`;
+        const protocols = parseProtocols(content);
+        expect(protocols).toHaveLength(1);
+        expect(protocols[0].id).toBe('PROTO-RFC-1');
+        expect(protocols[0].name).toBe('RFC Implementation');
+        expect(protocols[0].steps).toBe(6);
+        expect(protocols[0].automation_tier).toBe('automated');
+        expect(protocols[0].workflow).toBe('implement-rfc');
+        expect(protocols[0].tools).toEqual(['rfc:context', 'rfc:verify']);
+    });
+    it('parses multiple protocols', () => {
+        const content = `
+### PROTO-REV-1: Code Review
+
+1. Load constraints
+2. Check violations
+3. Report
+
+### PROTO-DEP-1: Deploy
+
+1. Build
+2. Test
+3. Deploy
+4. Verify
+5. Monitor
+`;
+        const protocols = parseProtocols(content);
+        expect(protocols).toHaveLength(2);
+        expect(protocols[0].id).toBe('PROTO-REV-1');
+        expect(protocols[1].id).toBe('PROTO-DEP-1');
+    });
+    it('infers complexity from steps and tier', () => {
+        const content = `
+### PROTO-SIMPLE-1: Simple Task
+
+1. Do thing
+
+### PROTO-COMPLEX-1: Complex Task
+
+1. Step 1
+2. Step 2
+3. Step 3
+4. Step 4
+5. Step 5
+6. Step 6
+7. Step 7
+8. Step 8
+`;
+        const protocols = parseProtocols(content);
+        expect(protocols[0].complexity).toBe('low');
+        expect(protocols[1].complexity).toBe('high');
+    });
+    it('returns empty for no protocols', () => {
+        const content = '# Just a heading\n\nSome content.';
+        const protocols = parseProtocols(content);
+        expect(protocols).toHaveLength(0);
+    });
+    it('defaults to manual automation tier', () => {
+        const content = `
+### PROTO-MAN-1: Manual Process
+
+1. Think about it
+2. Do it
+`;
+        const protocols = parseProtocols(content);
+        expect(protocols[0].automation_tier).toBe('manual');
+    });
+});
+//# sourceMappingURL=add-protocols-array.test.js.map

package/dist/core/add-protocols-array.test.js.map

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

@@ -0,0 +1,44 @@
+/**
+ * OrganonConfig resolution.
+ *
+ * Discovery order:
+ * 1. Explicit config file path (--config flag)
+ * 2. organon.config.json in projectRoot
+ * 3. Convention-based defaults (scan for organon/, .claude/skills/, etc.)
+ */
+import { z } from 'zod';
+import type { FileSystem, OrganonConfig } from './types.js';
+declare const ConfigFileSchema: z.ZodObject<{
+    methodology_version: z.ZodOptional<z.ZodString>;
+    organonPaths: z.ZodOptional<z.ZodArray<z.ZodString>>;
+    organonGlobs: z.ZodOptional<z.ZodArray<z.ZodString>>;
+    ignorePatterns: z.ZodOptional<z.ZodArray<z.ZodString>>;
+    workflowPaths: z.ZodOptional<z.ZodObject<{
+        claudeCode: z.ZodOptional<z.ZodString>;
+        cursor: z.ZodOptional<z.ZodString>;
+        generic: z.ZodOptional<z.ZodString>;
+    }, z.core.$strict>>;
+    freshnessThresholdHours: z.ZodOptional<z.ZodNumber>;
+    testGlobs: z.ZodOptional<z.ZodArray<z.ZodString>>;
+    testIgnorePatterns: z.ZodOptional<z.ZodArray<z.ZodString>>;
+}, z.core.$strict>;
+export type ConfigFile = z.infer<typeof ConfigFileSchema>;
+/**
+ * Resolve config by merging file-based config with convention defaults.
+ */
+export declare function resolveConfig(projectRoot: string, fs: FileSystem, configPath?: string): Promise<OrganonConfig>;
+/**
+ * Simple path join that handles both / and \ separators.
+ * Avoids importing node:path in the core module.
+ */
+export declare function joinPath(...segments: string[]): string;
+/**
+ * Get the directory portion of a path.
+ */
+export declare function dirName(path: string): string;
+/**
+ * Get the filename from a path.
+ */
+export declare function baseName(path: string): string;
+export {};
+//# sourceMappingURL=config.d.ts.map

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

@@ -0,0 +1 @@
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