@organon-methodology/tools 0.3.0

package/dist/core/types.d.ts

@@ -0,0 +1,277 @@
+/**
+ * Shared types for the Organon tools core.
+ *
+ * All core functions depend on these types. The FileSystem interface
+ * enables dependency injection for testability (in-memory fs for tests,
+ * NodeFileSystem for real I/O).
+ */
+export interface FileStat {
+    mtime: Date;
+    size: number;
+}
+export interface FileSystem {
+    readFile(path: string): Promise<string>;
+    readDir(path: string): Promise<string[]>;
+    exists(path: string): Promise<boolean>;
+    glob(pattern: string, options?: {
+        cwd: string;
+        ignore?: string[];
+    }): Promise<string[]>;
+    stat(path: string): Promise<FileStat>;
+}
+export type Severity = 'error' | 'warning' | 'info';
+export interface DiagnosticMessage {
+    severity: Severity;
+    code: string;
+    message: string;
+    file?: string;
+    line?: number;
+    suggestion?: string;
+}
+export type FrontmatterType = 'navigation' | 'constraints' | 'rationale' | 'procedures' | 'mapping';
+export type FrontmatterScope = 'product' | 'domain' | 'feature' | 'component' | 'meta' | 'methodology';
+export type AutomationTier = 'automated' | 'semi-automated' | 'manual';
+export type LoadPriority = 'high' | 'medium' | 'low';
+export type Complexity = 'high' | 'medium' | 'low';
+export type Audience = 'llm' | 'human' | 'tooling';
+export interface ProtocolEntry {
+    id: string;
+    name: string;
+    steps: number;
+    automation_tier: AutomationTier;
+    workflow?: string;
+    tools?: string[];
+    complexity: Complexity;
+}
+export interface InvariantEntry {
+    id: string;
+    name: string;
+    judgment_call?: boolean;
+}
+/**
+ * Union of all possible frontmatter fields.
+ * Not every file will have every field — type-specific fields
+ * are validated based on the `type` value.
+ */
+export interface Frontmatter {
+    type: FrontmatterType;
+    scope: FrontmatterScope;
+    name: string;
+    version: string;
+    summary: string;
+    token_estimate: number;
+    invariants_count?: number;
+    principles_count?: number;
+    heuristics_count?: number;
+    invariants?: InvariantEntry[];
+    decision_count?: number;
+    explains_invariants?: string[];
+    protocols_count?: number;
+    protocols?: ProtocolEntry[];
+    provides?: string[];
+    parent?: string;
+    file_count?: number;
+    last_generated?: string;
+    inherits_from?: string[];
+    related_domains?: string[];
+    related_features?: string[];
+    primary_rfcs?: number[];
+    secondary_rfcs?: number[];
+    load_priority?: LoadPriority;
+    required_for?: string[];
+    audience?: Audience[];
+    last_reviewed?: string;
+    methodology_version?: string;
+    [key: string]: unknown;
+}
+export interface ParsedOrganonFile {
+    /** Absolute or project-relative path */
+    path: string;
+    /** Parsed frontmatter, or null if missing/invalid */
+    frontmatter: Frontmatter | null;
+    /** Raw YAML string (between --- delimiters) */
+    rawFrontmatter: string;
+    /** File content after frontmatter */
+    body: string;
+    /** Full file content */
+    content: string;
+}
+export interface ValidateFrontmatterResult {
+    success: boolean;
+    filesChecked: number;
+    filesWithErrors: number;
+    filesWithWarnings: number;
+    results: FileValidationResult[];
+    errors: DiagnosticMessage[];
+    warnings: DiagnosticMessage[];
+}
+export interface FileValidationResult {
+    file: string;
+    valid: boolean;
+    errors: DiagnosticMessage[];
+    warnings: DiagnosticMessage[];
+}
+export interface GenerateFrontmatterResult {
+    success: boolean;
+    file: string;
+    generated: Partial<Frontmatter>;
+    errors: DiagnosticMessage[];
+    warnings: DiagnosticMessage[];
+}
+export interface QueryResult {
+    success: boolean;
+    files: ParsedOrganonFile[];
+    totalTokens: number;
+    errors: DiagnosticMessage[];
+    warnings: DiagnosticMessage[];
+}
+export interface HealthResult {
+    success: boolean;
+    score: number;
+    coverage: {
+        totalFiles: number;
+        withFrontmatter: number;
+        percentage: number;
+    };
+    validation: {
+        passing: number;
+        failing: number;
+        warnings: number;
+    };
+    tokens: {
+        total: number;
+        average: number;
+        largest: {
+            file: string;
+            tokens: number;
+        };
+        smallest: {
+            file: string;
+            tokens: number;
+        };
+    };
+    freshness: {
+        fresh: number;
+        stale: number;
+        unknown: number;
+        stalestFile?: {
+            file: string;
+            lastModified: Date;
+        };
+    };
+    issues: DiagnosticMessage[];
+    errors: DiagnosticMessage[];
+    warnings: DiagnosticMessage[];
+}
+export interface FindResult {
+    success: boolean;
+    mode: 'by-file' | 'by-scope' | 'by-type' | 'by-name';
+    matches: FindMatch[];
+    errors: DiagnosticMessage[];
+    warnings: DiagnosticMessage[];
+}
+export interface FindMatch {
+    file: string;
+    frontmatter: Frontmatter | null;
+    relevance: string;
+}
+export interface VerifyTripletsResult {
+    success: boolean;
+    bindings: TripletBinding[];
+    orphanedWorkflows: string[];
+    phantomAutomation: string[];
+    errors: DiagnosticMessage[];
+    warnings: DiagnosticMessage[];
+}
+export interface TripletBinding {
+    protocolId: string;
+    protocolFile: string;
+    automationTier: AutomationTier;
+    workflowName?: string;
+    workflowFile?: string;
+    tools?: string[];
+    valid: boolean;
+    issues: DiagnosticMessage[];
+}
+export interface WorkflowValidationResult {
+    success: boolean;
+    workflowsChecked: number;
+    workflowsWithErrors: number;
+    workflowsWithWarnings: number;
+    results: WorkflowFileResult[];
+    errors: DiagnosticMessage[];
+    warnings: DiagnosticMessage[];
+}
+export interface WorkflowFileResult {
+    file: string;
+    valid: boolean;
+    errors: DiagnosticMessage[];
+    warnings: DiagnosticMessage[];
+}
+export interface SuggestToolsResult {
+    success: boolean;
+    suggestions: ToolSuggestion[];
+    errors: DiagnosticMessage[];
+    warnings: DiagnosticMessage[];
+}
+export interface ToolSuggestion {
+    protocolId: string;
+    protocolFile: string;
+    currentTier: AutomationTier;
+    suggestedTier: AutomationTier;
+    reason: string;
+    steps: number;
+    complexity: Complexity;
+}
+export interface VerifyGateResult {
+    gate: string;
+    passed: boolean;
+    errors: DiagnosticMessage[];
+    warnings: DiagnosticMessage[];
+}
+export interface VerifyResult {
+    success: boolean;
+    gates: VerifyGateResult[];
+    errors: DiagnosticMessage[];
+    warnings: DiagnosticMessage[];
+}
+export type VerifyGateFn = (options: {
+    projectRoot: string;
+    config: OrganonConfig;
+    fs: FileSystem;
+}) => Promise<VerifyGateResult>;
+export interface InvariantCoverageResult {
+    success: boolean;
+    invariants: InvariantCoverageEntry[];
+    summary: {
+        total: number;
+        covered: number;
+        uncovered: number;
+        judgment_call: number;
+    };
+    errors: DiagnosticMessage[];
+    warnings: DiagnosticMessage[];
+}
+export interface InvariantCoverageEntry {
+    id: string;
+    name: string;
+    file: string;
+    status: 'covered' | 'uncovered' | 'judgment_call';
+    tests: string[];
+}
+export interface WorkflowPaths {
+    claudeCode?: string;
+    cursor?: string;
+    generic?: string;
+}
+export interface OrganonConfig {
+    projectRoot: string;
+    organonPaths: string[];
+    organonGlobs: string[];
+    ignorePatterns: string[];
+    workflowPaths: WorkflowPaths;
+    freshnessThresholdHours: number;
+    testGlobs?: string[];
+    testIgnorePatterns?: string[];
+}
+//# sourceMappingURL=types.d.ts.map

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

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package/dist/core/types.js

@@ -0,0 +1,9 @@
+/**
+ * Shared types for the Organon tools core.
+ *
+ * All core functions depend on these types. The FileSystem interface
+ * enables dependency injection for testability (in-memory fs for tests,
+ * NodeFileSystem for real I/O).
+ */
+export {};
+//# sourceMappingURL=types.js.map

package/dist/core/types.js.map

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

@@ -0,0 +1,46 @@
+/**
+ * Pure upgrade logic for `organon upgrade`.
+ *
+ * Detects version drift, computes upgrade plan, and applies changes.
+ * Each function is pure, composable, and testable.
+ *
+ * @organon-invariant INV-TOOLS-5 idempotent-operations
+ */
+import type { FileSystem, DiagnosticMessage } from './types.js';
+export interface UpgradeOptions {
+    projectRoot: string;
+    skillsOnly: boolean;
+    fs: FileSystem;
+}
+export interface VersionInfo {
+    /** Current methodology version (null = pre-versioning or not found) */
+    current: string | null;
+    /** CLI's bundled methodology version */
+    target: string;
+    /** Type of drift */
+    drift: 'none' | 'behind' | 'ahead' | 'unknown';
+}
+export interface UpgradeChange {
+    type: 'skill' | 'config' | 'structure';
+    action: 'create' | 'update';
+    path: string;
+    description: string;
+}
+export interface UpgradePlan {
+    version: VersionInfo;
+    changes: UpgradeChange[];
+}
+export interface UpgradeResult {
+    success: boolean;
+    plan: UpgradePlan;
+    applied: string[];
+    diagnostics: DiagnosticMessage[];
+    /** Files to write: relative path → content */
+    filesToWrite: Map<string, string>;
+}
+export declare function detectVersion(projectRoot: string, fs: FileSystem): Promise<VersionInfo>;
+export declare function computeUpgradePlan(options: UpgradeOptions & {
+    version: VersionInfo;
+}): Promise<UpgradePlan>;
+export declare function applyUpgrade(plan: UpgradePlan, projectRoot: string, fs: FileSystem): Promise<UpgradeResult>;
+//# sourceMappingURL=upgrade.d.ts.map

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

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package/dist/core/upgrade.js

@@ -0,0 +1,227 @@
+/**
+ * Pure upgrade logic for `organon upgrade`.
+ *
+ * Detects version drift, computes upgrade plan, and applies changes.
+ * Each function is pure, composable, and testable.
+ *
+ * @organon-invariant INV-TOOLS-5 idempotent-operations
+ */
+import { joinPath } from './config.js';
+import { getSkillTemplates, METHODOLOGY_VERSION, CONFIG_TEMPLATE, } from '../templates/index.js';
+// ---------------------------------------------------------------------------
+// Version detection
+// ---------------------------------------------------------------------------
+export async function detectVersion(projectRoot, fs) {
+    const target = METHODOLOGY_VERSION;
+    // Try reading methodology_version from organon.config.json
+    const configPath = joinPath(projectRoot, 'organon.config.json');
+    let current = null;
+    try {
+        if (await fs.exists(configPath)) {
+            const raw = await fs.readFile(configPath);
+            const config = JSON.parse(raw);
+            if (typeof config.methodology_version === 'string') {
+                current = config.methodology_version;
+            }
+        }
+    }
+    catch {
+        // Config doesn't exist or isn't valid JSON — treat as pre-versioning
+    }
+    let drift;
+    if (current === null) {
+        drift = 'unknown';
+    }
+    else if (current === target) {
+        drift = 'none';
+    }
+    else if (compareSemver(current, target) < 0) {
+        drift = 'behind';
+    }
+    else {
+        drift = 'ahead';
+    }
+    return { current, target, drift };
+}
+// ---------------------------------------------------------------------------
+// Upgrade plan computation
+// ---------------------------------------------------------------------------
+export async function computeUpgradePlan(options) {
+    const { projectRoot, skillsOnly, fs, version } = options;
+    const changes = [];
+    // Skill changes
+    const skillTemplates = getSkillTemplates();
+    for (const [skillName, { path: relativePath, content }] of skillTemplates) {
+        try {
+            const fullPath = joinPath(projectRoot, relativePath);
+            const exists = await fs.exists(fullPath);
+            if (!exists) {
+                changes.push({
+                    type: 'skill',
+                    action: 'create',
+                    path: relativePath,
+                    description: `New skill: ${skillName}`,
+                });
+            }
+            else {
+                // Compare content
+                try {
+                    const existing = await fs.readFile(fullPath);
+                    if (normalizeContent(existing) !== normalizeContent(content)) {
+                        changes.push({
+                            type: 'skill',
+                            action: 'update',
+                            path: relativePath,
+                            description: `Updated: ${skillName}`,
+                        });
+                    }
+                }
+                catch {
+                    // Can't read — treat as needing update
+                    changes.push({
+                        type: 'skill',
+                        action: 'update',
+                        path: relativePath,
+                        description: `Updated: ${skillName} (could not read existing)`,
+                    });
+                }
+            }
+        }
+        catch {
+            // Can't check existence — treat as needing create
+            changes.push({
+                type: 'skill',
+                action: 'create',
+                path: relativePath,
+                description: `New skill: ${skillName} (could not check existing)`,
+            });
+        }
+    }
+    // Config changes (skip if skills-only)
+    if (!skillsOnly) {
+        try {
+            const configPath = joinPath(projectRoot, 'organon.config.json');
+            const configExists = await fs.exists(configPath);
+            if (!configExists) {
+                changes.push({
+                    type: 'config',
+                    action: 'create',
+                    path: 'organon.config.json',
+                    description: 'Create organon.config.json with methodology_version',
+                });
+            }
+            else if (version.drift === 'behind' || version.drift === 'unknown') {
+                changes.push({
+                    type: 'config',
+                    action: 'update',
+                    path: 'organon.config.json',
+                    description: `Update methodology_version: ${version.current ?? '(none)'} → ${version.target}`,
+                });
+            }
+        }
+        catch {
+            // Can't check config — suggest creating it
+            changes.push({
+                type: 'config',
+                action: 'create',
+                path: 'organon.config.json',
+                description: 'Create organon.config.json (could not check existing)',
+            });
+        }
+    }
+    return { version, changes };
+}
+// ---------------------------------------------------------------------------
+// Apply upgrade
+// ---------------------------------------------------------------------------
+export async function applyUpgrade(plan, projectRoot, fs) {
+    const applied = [];
+    const diagnostics = [];
+    // Collect files to write
+    const filesToWrite = new Map();
+    const skillTemplates = getSkillTemplates();
+    for (const change of plan.changes) {
+        if (change.type === 'skill') {
+            const skill = [...skillTemplates.values()].find((s) => s.path === change.path);
+            if (skill) {
+                filesToWrite.set(change.path, skill.content);
+                applied.push(change.path);
+            }
+            else {
+                diagnostics.push({
+                    severity: 'warning',
+                    code: 'UPGRADE_SKILL_TEMPLATE_NOT_FOUND',
+                    message: `Skill template not found for path: ${change.path}`,
+                    file: change.path,
+                });
+            }
+        }
+        else if (change.type === 'structure') {
+            // Structure changes not yet implemented — report as diagnostic
+            diagnostics.push({
+                severity: 'warning',
+                code: 'UPGRADE_STRUCTURE_NOT_SUPPORTED',
+                message: `Structure change not applied (not yet supported): ${change.description}`,
+                file: change.path,
+            });
+        }
+        else if (change.type === 'config') {
+            if (change.action === 'create') {
+                filesToWrite.set('organon.config.json', CONFIG_TEMPLATE);
+                applied.push('organon.config.json');
+            }
+            else if (change.action === 'update') {
+                // Update methodology_version in existing config
+                const configPath = joinPath(projectRoot, 'organon.config.json');
+                try {
+                    const raw = await fs.readFile(configPath);
+                    const config = JSON.parse(raw);
+                    config.methodology_version = plan.version.target;
+                    filesToWrite.set('organon.config.json', JSON.stringify(config, null, 2) + '\n');
+                    applied.push('organon.config.json');
+                }
+                catch (err) {
+                    diagnostics.push({
+                        severity: 'error',
+                        code: 'UPGRADE_CONFIG_READ_ERROR',
+                        message: `Could not update config: ${err instanceof Error ? err.message : String(err)}`,
+                        file: 'organon.config.json',
+                    });
+                }
+            }
+        }
+    }
+    return {
+        success: diagnostics.filter((d) => d.severity === 'error').length === 0,
+        plan,
+        applied,
+        diagnostics,
+        filesToWrite,
+    };
+}
+// ---------------------------------------------------------------------------
+// Helpers
+// ---------------------------------------------------------------------------
+/** Normalize content for comparison (trim, normalize line endings). */
+function normalizeContent(content) {
+    return content.replace(/\r\n/g, '\n').trim();
+}
+/** Simple semver comparison. Returns -1, 0, or 1. Strips pre-release suffixes. */
+function compareSemver(a, b) {
+    // Strip pre-release suffix (e.g., "0.3.0-beta.1" → "0.3.0")
+    const clean = (v) => v.replace(/-.*$/, '');
+    const pa = clean(a).split('.').map(Number);
+    const pb = clean(b).split('.').map(Number);
+    for (let i = 0; i < 3; i++) {
+        const va = pa[i] ?? 0;
+        const vb = pb[i] ?? 0;
+        if (Number.isNaN(va) || Number.isNaN(vb))
+            return 0;
+        if (va < vb)
+            return -1;
+        if (va > vb)
+            return 1;
+    }
+    return 0;
+}
+//# sourceMappingURL=upgrade.js.map

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

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

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

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