@organon-methodology/tools 0.3.0

package/LICENSE

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+MIT License
+
+Copyright (c) 2025 Organon Methodology Contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

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+---
+type: navigation
+scope: domain
+name: tools
+version: "1.0"
+summary: CLI and MCP server for the Organon methodology — validate frontmatter, run verification gates, query organon files
+token_estimate: 1700
+provides: [architecture, cli-commands, mcp-server, configuration, programmatic-api]
+parent: packages
+audience: [llm, human]
+---
+
+# Organon Tools
+
+CLI tools and MCP server for the **Organon Methodology** — enforce documentation constraints, validate frontmatter, and give agents immediate methodology context.
+
+## Organon (Start Here)
+
+This project uses the Organon methodology to govern its own development:
+
+- **[ETHOS.md](../../organon/domains/tools/ETHOS.md)** — Constraints for developing organon-tools (what rules must never be violated)
+- **[PHILOSOPHY.md](../../organon/domains/tools/PHILOSOPHY.md)** — Design decisions and trade-offs (why TypeScript, why CLI, why fail-fast)
+- **[dev/](./dev/)** — Design docs, RFCs, and future tool ideas
+
+**For contributors:** Read ETHOS.md first to understand invariants and principles. Read PHILOSOPHY.md to understand why the tool is built this way.
+
+## Architecture
+
+```
+packages/tools/src/
+├── core/               ← Pure logic (no I/O, no console, no process.exit)
+│   ├── types.ts        ← FileSystem interface, result types, config
+│   ├── config.ts       ← Convention-based config discovery
+│   ├── frontmatter-parser.ts
+│   ├── node-fs.ts      ← NodeFileSystem implementation
+│   ├── validate-frontmatter.ts   ← 4-stage validation
+│   ├── generate-frontmatter.ts   ← Auto-generate from content
+│   ├── query.ts        ← Filter by scope/type/priority/budget
+│   ├── health.ts       ← Coverage, validation, tokens, freshness
+│   ├── find.ts         ← Cross-domain discovery
+│   ├── verify-triplets.ts  ← Protocol↔workflow↔tool bindings
+│   ├── suggest-tools.ts    ← Automation tier suggestions
+│   └── verify.ts       ← Gate registry orchestrator
+├── cli/                ← Thin yargs adapter
+│   └── commands/       ← validate, generate, query, health, find, verify, mcp
+├── mcp/                ← Thin MCP adapter
+│   ├── server.ts       ← stdio transport
+│   ├── tools.ts        ← 8 MCP tools
+│   ├── resources.ts    ← 4 MCP resources
+│   └── prompts.ts      ← 4 MCP prompts
+└── index.ts            ← Public API
+```
+
+## CLI Commands
+
+```bash
+# Validate frontmatter (schema, references, truthfulness, consistency)
+organon validate
+organon validate book-llms/ETHOS.md
+organon validate --stages 1 3
+
+# Generate frontmatter from file content
+organon generate book-llms/ETHOS.md
+organon generate book-llms/ETHOS.md --update
+
+# Query organon files by metadata
+organon query --scope=meta
+organon query --budget=20000
+organon query --task=genesis_tool_impl
+
+# Health dashboard
+organon health
+organon health --detailed --fix-suggestions
+
+# Cross-domain discovery
+organon find --file=src/domain/genesis/Store.ts
+organon find --scope=domain
+organon find --name=frontmatter
+
+# Run verification gates
+organon verify
+organon verify --gate frontmatter triplets
+
+# Start MCP server
+organon mcp
+```
+
+## MCP Server
+
+Start with `organon mcp`. Exposes:
+
+**8 Tools:** `organon_validate_frontmatter`, `organon_generate_frontmatter`, `organon_query`, `organon_health`, `organon_find`, `organon_verify_triplets`, `organon_suggest_tools`, `organon_verify`
+
+**4 Resources:** `organon://index`, `organon://file/{path}`, `organon://scope/{scope}`, `organon://health`
+
+**4 Prompts:** `implement-feature`, `review-changes`, `create-organon`, `evolve-organon`
+
+### Claude Code Integration
+
+```json
+{
+  "mcpServers": {
+    "organon": {
+      "command": "npx",
+      "args": ["tsx", "packages/tools/src/cli/index.ts", "mcp", "--project-root", "."]
+    }
+  }
+}
+```
+
+## Configuration
+
+Place `organon.config.json` at your project root:
+
+```json
+{
+  "organonPaths": ["book-llms", "organon", "."],
+  "organonGlobs": ["**/ETHOS.md", "**/PHILOSOPHY.md", "**/PROTOCOL.md", "**/README.md"],
+  "ignorePatterns": ["node_modules/**", "dist/**"],
+  "workflowPaths": {
+    "claudeCode": ".claude/skills",
+    "cursor": ".cursor/rules"
+  },
+  "freshnessThresholdHours": 720
+}
+```
+
+Without a config file, conventions are used: scans for `organon/` and `book-llms/` directories automatically.
+
+## Programmatic API
+
+```typescript
+import { validateFrontmatter, resolveConfig, NodeFileSystem } from '@organon-methodology/tools';
+
+const fs = new NodeFileSystem();
+const config = await resolveConfig('.', fs);
+const result = await validateFrontmatter({ projectRoot: '.', config, fs });
+```
+
+## Development
+
+```bash
+npm install
+npm run build
+npm run dev          # watch mode
+npm test             # vitest
+npm run organon      # run CLI locally
+```
+
+## License
+
+MIT

package/dist/cli/commands/coverage.d.ts

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+/**
+ * organon coverage — Invariant coverage analysis.
+ */
+import type { CommandModule } from 'yargs';
+interface CoverageArgs {
+    'project-root': string;
+    config?: string;
+    json: boolean;
+}
+export declare const coverageCommand: CommandModule<{}, CoverageArgs>;
+export {};
+//# sourceMappingURL=coverage.d.ts.map

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

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package/dist/cli/commands/coverage.js

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+/**
+ * organon coverage — Invariant coverage analysis.
+ */
+import chalk from 'chalk';
+import { resolveConfig } from '../../core/config.js';
+import { computeInvariantCoverage } from '../../core/invariant-coverage.js';
+import { NodeFileSystem } from '../../core/node-fs.js';
+export const coverageCommand = {
+    command: 'coverage',
+    describe: 'Analyze invariant test coverage',
+    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('json', {
+            describe: 'Output machine-readable JSON',
+            type: 'boolean',
+            default: false,
+        })
+            .example('$0 coverage', 'Show invariant coverage report')
+            .example('$0 coverage --json', 'Output coverage as JSON');
+    },
+    handler: async (args) => {
+        const fs = new NodeFileSystem();
+        const config = await resolveConfig(args['project-root'], fs, args.config);
+        const result = await computeInvariantCoverage({
+            projectRoot: args['project-root'],
+            config,
+            fs,
+        });
+        if (args.json) {
+            console.log(JSON.stringify(result, null, 2));
+        }
+        else {
+            console.log(chalk.blue('Organon Invariant Coverage'));
+            console.log();
+            if (result.invariants.length === 0) {
+                console.log(chalk.dim('  No invariants defined in frontmatter.'));
+                console.log(chalk.dim('  Add an `invariants` array to ETHOS.md frontmatter.'));
+                return;
+            }
+            // Table header
+            console.log(`  ${chalk.dim('ID'.padEnd(18))}${chalk.dim('Name'.padEnd(30))}${chalk.dim('Status'.padEnd(16))}${chalk.dim('Tests')}`);
+            console.log(chalk.dim('  ' + '─'.repeat(74)));
+            for (const inv of result.invariants) {
+                const statusIcon = inv.status === 'covered' ? chalk.green('covered')
+                    : inv.status === 'judgment_call' ? chalk.yellow('judgment')
+                        : chalk.red('uncovered');
+                const tests = inv.tests.length > 0 ? inv.tests.join(', ') : chalk.dim('none');
+                console.log(`  ${inv.id.padEnd(18)}${inv.name.padEnd(30)}${statusIcon.padEnd(16)}${tests}`);
+            }
+            console.log();
+            const { summary } = result;
+            const parts = [
+                `${summary.covered}/${summary.total} covered`,
+            ];
+            if (summary.judgment_call > 0) {
+                parts.push(`${summary.judgment_call} judgment calls`);
+            }
+            if (summary.uncovered > 0) {
+                parts.push(`${summary.uncovered} uncovered`);
+            }
+            if (result.success) {
+                console.log(chalk.green(`  ✓ ${parts.join(', ')}`));
+            }
+            else {
+                console.log(chalk.red(`  ✗ ${parts.join(', ')}`));
+                process.exit(1);
+            }
+        }
+    },
+};
+//# sourceMappingURL=coverage.js.map

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package/dist/cli/commands/find.d.ts

@@ -0,0 +1,15 @@
+/**
+ * organon find — Cross-domain discovery.
+ */
+import type { CommandModule } from 'yargs';
+interface FindArgs {
+    'project-root': string;
+    config?: string;
+    file?: string;
+    scope?: string;
+    type?: string;
+    name?: string;
+}
+export declare const findCommand: CommandModule<{}, FindArgs>;
+export {};
+//# sourceMappingURL=find.d.ts.map

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package/dist/cli/commands/find.js

@@ -0,0 +1,81 @@
+/**
+ * organon find — Cross-domain discovery.
+ */
+import chalk from 'chalk';
+import { resolveConfig } from '../../core/config.js';
+import { find } from '../../core/find.js';
+import { NodeFileSystem } from '../../core/node-fs.js';
+export const findCommand = {
+    command: 'find',
+    describe: 'Cross-domain discovery (find organons by file, scope, type, or name)',
+    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('file', {
+            describe: 'Find organons governing this file path',
+            type: 'string',
+        })
+            .option('scope', {
+            describe: 'List organons at this scope level',
+            type: 'string',
+            choices: ['product', 'domain', 'feature', 'component', 'meta', 'methodology'],
+        })
+            .option('type', {
+            describe: 'List organons of this type',
+            type: 'string',
+            choices: ['navigation', 'constraints', 'rationale', 'procedures', 'mapping'],
+        })
+            .option('name', {
+            describe: 'Find organons matching this name (substring)',
+            type: 'string',
+        })
+            .check((argv) => {
+            if (!argv.file && !argv.scope && !argv.type && !argv.name) {
+                throw new Error('Specify at least one: --file, --scope, --type, or --name');
+            }
+            return true;
+        })
+            .example('$0 find --file=src/domain/genesis/Store.ts', 'Find governing organons')
+            .example('$0 find --scope=domain', 'List all domain organons')
+            .example('$0 find --name=frontmatter', 'Search by name');
+    },
+    handler: async (args) => {
+        const fs = new NodeFileSystem();
+        const config = await resolveConfig(args['project-root'], fs, args.config);
+        const result = await find({
+            projectRoot: args['project-root'],
+            config,
+            fs,
+            file: args.file,
+            scope: args.scope,
+            type: args.type,
+            name: args.name,
+        });
+        console.log(chalk.blue('Organon Find'));
+        console.log(chalk.dim(`  Mode: ${result.mode}`));
+        console.log();
+        if (result.matches.length === 0) {
+            console.log(chalk.yellow('  No matches found'));
+        }
+        else {
+            for (const match of result.matches) {
+                console.log(`  ${chalk.green(match.file)}`);
+                if (match.frontmatter) {
+                    console.log(chalk.dim(`    ${match.frontmatter.type} | ${match.frontmatter.scope} | ${match.frontmatter.name}`));
+                }
+                console.log(chalk.dim(`    ${match.relevance}`));
+            }
+        }
+        console.log();
+        console.log(chalk.dim(`${result.matches.length} match(es)`));
+    },
+};
+//# sourceMappingURL=find.js.map

package/dist/cli/commands/find.js.map

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package/dist/cli/commands/generate-tests.d.ts

@@ -0,0 +1,14 @@
+/**
+ * organon generate-tests — Generate test scaffolds for uncovered invariants.
+ */
+import type { CommandModule } from 'yargs';
+interface GenerateTestsArgs {
+    'project-root': string;
+    config?: string;
+    invariant?: string[];
+    'out-dir'?: string;
+    json: boolean;
+}
+export declare const generateTestsCommand: CommandModule<{}, GenerateTestsArgs>;
+export {};
+//# sourceMappingURL=generate-tests.d.ts.map

package/dist/cli/commands/generate-tests.d.ts.map

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package/dist/cli/commands/generate-tests.js

@@ -0,0 +1,87 @@
+/**
+ * organon generate-tests — Generate test scaffolds for uncovered invariants.
+ */
+import chalk from 'chalk';
+import { resolveConfig } from '../../core/config.js';
+import { generateTests } from '../../core/generate-tests.js';
+import { NodeFileSystem } from '../../core/node-fs.js';
+export const generateTestsCommand = {
+    command: 'generate-tests',
+    describe: 'Generate test scaffolds for uncovered invariants',
+    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('invariant', {
+            describe: 'Generate for specific invariant ID(s)',
+            type: 'array',
+            string: true,
+        })
+            .option('out-dir', {
+            describe: 'Directory to write generated test files',
+            type: 'string',
+        })
+            .option('json', {
+            describe: 'Output machine-readable JSON',
+            type: 'boolean',
+            default: false,
+        })
+            .example('$0 generate-tests', 'Generate scaffolds for all uncovered invariants')
+            .example('$0 generate-tests --invariant INV-FOO-1', 'Generate for specific invariant')
+            .example('$0 generate-tests --json', 'Output as JSON');
+    },
+    handler: async (args) => {
+        const fs = new NodeFileSystem();
+        const config = await resolveConfig(args['project-root'], fs, args.config);
+        const result = await generateTests({
+            projectRoot: args['project-root'],
+            config,
+            fs,
+            invariantIds: args.invariant,
+            outDir: args['out-dir'],
+        });
+        if (args.json) {
+            console.log(JSON.stringify(result, null, 2));
+            return;
+        }
+        console.log(chalk.blue('Organon Generate Tests'));
+        console.log();
+        if (result.generated.length === 0 && result.alreadyCovered.length === 0 && result.judgmentCalls.length === 0) {
+            console.log(chalk.dim('  No invariants found. Add invariants to ETHOS.md frontmatter.'));
+            return;
+        }
+        // Show already covered
+        if (result.alreadyCovered.length > 0) {
+            console.log(chalk.green(`  ✓ ${result.alreadyCovered.length} invariant(s) already covered`));
+        }
+        // Show judgment calls
+        if (result.judgmentCalls.length > 0) {
+            console.log(chalk.yellow(`  ○ ${result.judgmentCalls.length} judgment call(s) (no test needed)`));
+        }
+        // Show generated scaffolds
+        if (result.generated.length > 0) {
+            console.log(chalk.cyan(`  ⚡ ${result.generated.length} test scaffold(s) generated:`));
+            console.log();
+            for (const test of result.generated) {
+                console.log(chalk.dim(`  ─── ${test.invariant.id}: ${test.invariant.name} ───`));
+                console.log(chalk.dim(`  Suggested assertion: ${test.assertion}`));
+                console.log(chalk.dim(`  Suggested filename: ${test.filename}`));
+                console.log();
+                console.log(test.code);
+                console.log();
+            }
+        }
+        else {
+            console.log();
+            console.log(chalk.green('  All invariants are covered!'));
+        }
+    },
+};
+//# sourceMappingURL=generate-tests.js.map

package/dist/cli/commands/generate-tests.js.map

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package/dist/cli/commands/generate.d.ts

@@ -0,0 +1,15 @@
+/**
+ * organon generate — Auto-generate frontmatter from file content.
+ */
+import type { CommandModule } from 'yargs';
+interface GenerateArgs {
+    file: string;
+    'project-root': string;
+    config?: string;
+    update?: boolean;
+    type?: string;
+    scope?: string;
+}
+export declare const generateCommand: CommandModule<{}, GenerateArgs>;
+export {};
+//# sourceMappingURL=generate.d.ts.map

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

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

@@ -0,0 +1,77 @@
+/**
+ * organon generate — Auto-generate frontmatter from file content.
+ */
+import chalk from 'chalk';
+import { resolveConfig } from '../../core/config.js';
+import { generateFrontmatter, serializeFrontmatter } from '../../core/generate-frontmatter.js';
+import { NodeFileSystem } from '../../core/node-fs.js';
+export const generateCommand = {
+    command: 'generate <file>',
+    describe: 'Auto-generate frontmatter for an organon file',
+    builder: (yargs) => {
+        return yargs
+            .positional('file', {
+            describe: 'File to generate frontmatter for',
+            type: 'string',
+            demandOption: true,
+        })
+            .option('project-root', {
+            describe: 'Project root directory',
+            type: 'string',
+            default: process.cwd(),
+        })
+            .option('config', {
+            describe: 'Path to organon.config.json',
+            type: 'string',
+        })
+            .option('update', {
+            describe: 'Write generated frontmatter back to file',
+            type: 'boolean',
+            default: false,
+        })
+            .option('type', {
+            describe: 'Override auto-detected type',
+            type: 'string',
+            choices: ['navigation', 'constraints', 'rationale', 'procedures', 'mapping'],
+        })
+            .option('scope', {
+            describe: 'Override auto-detected scope',
+            type: 'string',
+            choices: ['product', 'domain', 'feature', 'component', 'meta', 'methodology'],
+        })
+            .example('$0 generate book-llms/ETHOS.md', 'Generate frontmatter (dry run)')
+            .example('$0 generate book-llms/ETHOS.md --update', 'Generate and write to file');
+    },
+    handler: async (args) => {
+        const fs = new NodeFileSystem();
+        const config = await resolveConfig(args['project-root'], fs, args.config);
+        const result = await generateFrontmatter({
+            projectRoot: args['project-root'],
+            config,
+            fs,
+            file: args.file,
+            update: args.update,
+            type: args.type,
+            scope: args.scope,
+        });
+        console.log(chalk.blue('Organon Generate'));
+        console.log();
+        if (!result.success) {
+            for (const e of result.errors) {
+                console.log(chalk.red(`  ✗ [${e.code}] ${e.message}`));
+            }
+            process.exit(1);
+        }
+        const yaml = serializeFrontmatter(result.generated);
+        console.log(chalk.dim('Generated frontmatter:'));
+        console.log();
+        console.log(yaml);
+        if (args.update) {
+            console.log(chalk.green(`✓ Updated ${args.file}`));
+        }
+        else {
+            console.log(chalk.dim('(dry run — use --update to write)'));
+        }
+    },
+};
+//# sourceMappingURL=generate.js.map

package/dist/cli/commands/generate.js.map

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

@@ -0,0 +1,13 @@
+/**
+ * organon health — Dashboard showing coverage, validation, tokens, freshness.
+ */
+import type { CommandModule } from 'yargs';
+interface HealthArgs {
+    'project-root': string;
+    config?: string;
+    detailed?: boolean;
+    'fix-suggestions'?: boolean;
+}
+export declare const healthCommand: CommandModule<{}, HealthArgs>;
+export {};
+//# sourceMappingURL=health.d.ts.map

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

@@ -0,0 +1 @@
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