ai-factory 2.10.0 → 2.12.0

package/README.md

@@ -33,7 +33,7 @@ ai-factory init
 - **Spec-driven development** — AI follows plans, not random exploration. Predictable, resumable, reviewable
 - **Community skills** — leverage [skills.sh](https://skills.sh) ecosystem or generate custom skills
 - **Stack-agnostic** — works with any language, framework, or platform
-- **Multi-agent support** — Claude Code, Cursor, Windsurf, Roo Code, Kilo Code, Antigravity, OpenCode, Warp, Zencoder, Codex CLI, GitHub Copilot, Gemini CLI, Junie, Qwen Code, or [any agent](docs/getting-started.md#supported-agents)
+- **Multi-agent support** — Claude Code, Cursor, Windsurf, Roo Code, Kilo Code, Antigravity, OpenCode, Warp, Zencoder, Codex CLI, Codex app, GitHub Copilot, Gemini CLI, Junie, Qwen Code, or [any agent](docs/getting-started.md#supported-agents)
 
 ---
 
@@ -72,46 +72,11 @@ Then open your AI agent and start working:
 /aif
 ```
 
-## Usage
+Codex CLI and Codex app use `$aif` style invocations after installation.
 
-If the package is installed:
-```bash
-ai-factory init
-```
+Need CLI flags, update/upgrade details, or extension commands? See [Getting Started](docs/getting-started.md). Need slash-command reference? See [Core Skills](docs/skills.md).
 
-Or running without installation via `npx`:
-```bash
-npx ai-factory init
-```
-
-### Non-interactive mode
-
-Pass `--agents` to skip the interactive wizard:
-
-```bash
-# Agents + MCP servers
-ai-factory init --agents claude,cursor --mcp github,playwright
-
-# With specific skills
-ai-factory init --agents claude --skills commit,plan
-
-# Without base skills
-ai-factory init --agents codex --no-skills --mcp github
-```
-
-Available MCP servers: `github`, `postgres`, `filesystem`, `chrome-devtools`, `playwright`
-
-### Upgrading from v1 to v2
-
-```bash
-ai-factory upgrade
-```
-
-`ai-factory upgrade` removes old bare-named skills (`commit`, `feature`, etc.) and installs new `aif-*` prefixed versions. Custom skills are preserved.
-
-> **Note:** `ai-factory update` automatically checks npm for a newer CLI version and offers to install it before updating skills, then reports `changed/unchanged/skipped/removed` for installed base skills. Use `ai-factory update --force` for a clean reinstall of currently installed base skills.
-
-### Example Workflow
+## Example Workflow
 
 ```bash
 # Explore options and requirements before planning (optional)
@@ -144,20 +109,6 @@ ai-factory upgrade
 
 See the full [Development Workflow](docs/workflow.md) with diagram and decision table.
 
-### Auto-Generated Documentation
-
-AI Factory can generate and maintain your project docs with a single command:
-
-```bash
-/aif-docs          # Creates README + docs/ structure from your codebase
-/aif-docs --web    # Also generates a static HTML documentation site
-```
-
-- **Generates docs from scratch** — analyzes your codebase and creates a lean README + detailed `docs/` pages by topic
-- **Cleans up scattered files** — finds loose CONTRIBUTING.md, ARCHITECTURE.md, SETUP.md in your root and consolidates them into a structured `docs/` directory
-- **Keeps docs in sync** — integrates with `/aif-implement` docs policy (`Docs: yes` = mandatory docs checkpoint routed to `/aif-docs`, `Docs: no` = visible `WARN [docs]`)
-- **Builds a docs website** — `--web` generates a static HTML site with navigation and dark mode, ready to host
-
 ---
 
 ## Documentation
@@ -167,8 +118,9 @@ AI Factory can generate and maintain your project docs with a single command:
 | [Getting Started](docs/getting-started.md) | What is AI Factory, supported agents, CLI commands |
 | [Development Workflow](docs/workflow.md) | Workflow diagram, when to use `explore` vs `grounded`, spec-driven approach |
 | [Reflex Loop](docs/loop.md) | Iterative generate → evaluate → critique → refine workflow |
-| [Subagents](docs/subagents.md) | Claude Code only: repo-local planning, implementation, and loop subagents with narrow role contracts |
+| [Subagents](docs/subagents.md) | Bundled Claude subagents and the baseline Codex native agent-file bundle, including managed Codex config |
 | [Core Skills](docs/skills.md) | All slash commands — explore, grounded, plan, fix, implement, evolve, docs, and more |
+| [Quality Gates](docs/quality-gates.md) | Machine-readable `aif-gate-result` summaries for verify, review, security, and rules gates |
 | [Skill Evolution](docs/evolve.md) | How /aif-fix patches feed into /aif-evolve to generate smarter skill rules |
 | [Plan Files](docs/plan-files.md) | Plan files, self-improvement patches, skill acquisition |
 | [Security](docs/security.md) | Two-level security scanning for external skills |
@@ -176,22 +128,9 @@ AI Factory can generate and maintain your project docs with a single command:
 | [Configuration](docs/configuration.md) | `.ai-factory.json`, MCP servers, project structure, best practices |
 | [Config Reference](docs/config-reference.md) | Full `config.yaml` key reference and skill read/write matrix |
 
----
-
-![happy](https://github.com/ilhm344/ai-factory/blob/2.x/art/aif2.jpg)
-
-## AIF Handoff
-
-Looking for an **Autonomous Kanban board where AI agents plan, implement, and review your tasks**? Check out [aif-handoff](https://github.com/lee-to/aif-handoff) — a visual task management system built on top of AI Factory.
-
-![ui-light](https://github.com/lee-to/aif-handoff/blob/main/art/ui-light.png)
-![ui-dark](https://github.com/lee-to/aif-handoff/blob/main/art/ui-dark.png)
-![ui-light-list](https://github.com/lee-to/aif-handoff/blob/main/art/ui-light-list.png)
-![ui-dark-list](https://github.com/lee-to/aif-handoff/blob/main/art/ui-dark-list.png)
-
 ## Links
-
 - [Official Website](https://aif.cutcode.dev) - AI Factory website
+- [aif-handoff](https://github.com/lee-to/aif-handoff) - Autonomous Kanban board built on AI Factory
 - If AI Factory feels too simple for your goals, try [HLV](https://github.com/lee-to/hlv)
 - [skills.sh](https://skills.sh) - Skill marketplace
 - [Agent Skills Spec](https://agentskills.io) - Skill specification
@@ -204,6 +143,7 @@ Looking for an **Autonomous Kanban board where AI agents plan, implement, and re
 - [Warp](https://www.warp.dev) - Intelligent terminal with AI agent
 - [Zencoder](https://zencoder.ai) - AI coding agent for VS Code and JetBrains
 - [Codex CLI](https://github.com/openai/codex) - OpenAI's coding agent
+- [Codex app](https://openai.com/codex/) - OpenAI's coding agent app
 - [Gemini CLI](https://github.com/google-gemini/gemini-cli) - Google's coding agent
 - [Antigravity](https://antigravity.dev) - AI coding agent
 - [Junie](https://www.jetbrains.com/junie/) - JetBrains' AI coding agent

package/dist/cli/commands/audit-artifacts.d.ts

@@ -0,0 +1,7 @@
+interface AuditOptions {
+    json?: boolean;
+    strict?: boolean;
+}
+export declare function auditArtifactsCommand(paths?: string[], options?: AuditOptions): Promise<void>;
+export {};
+//# sourceMappingURL=audit-artifacts.d.ts.map

package/dist/cli/commands/audit-artifacts.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"audit-artifacts.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/audit-artifacts.ts"],"names":[],"mappings":"AAuBA,UAAU,YAAY;IACpB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AA2aD,wBAAsB,qBAAqB,CAAC,KAAK,GAAE,MAAM,EAAO,EAAE,OAAO,GAAE,YAAiB,GAAG,OAAO,CAAC,IAAI,CAAC,CA6C3G"}

package/dist/cli/commands/audit-artifacts.js

@@ -0,0 +1,407 @@
+import path from 'path';
+import fs from 'fs-extra';
+import chalk from 'chalk';
+import { readTextFile } from '../../utils/fs.js';
+const RELATION_FIELDS = [
+    'depends_on',
+    'affects',
+    'implements',
+    'verifies',
+    'documents',
+    'supersedes',
+];
+const DEFAULT_TARGETS = ['.ai-factory', 'docs', 'README.md', 'AGENTS.md'];
+const DEFAULT_SKIP_DIRS = new Set([
+    '.git',
+    'node_modules',
+    'dist',
+    'coverage',
+    'docs-html',
+    'evolution',
+    'evolutions',
+    'qa',
+]);
+function emptyRelations() {
+    return {
+        depends_on: [],
+        affects: [],
+        implements: [],
+        verifies: [],
+        documents: [],
+        supersedes: [],
+    };
+}
+function normalizeRelPath(projectDir, filePath) {
+    return path.relative(projectDir, filePath).replaceAll('\\', '/');
+}
+function isInsideProject(canonicalProjectDir, candidate) {
+    const relative = path.relative(canonicalProjectDir, candidate);
+    return relative === '' || (!relative.startsWith('..') && !path.isAbsolute(relative));
+}
+function stripInlineComment(value) {
+    const hashIndex = value.indexOf(' #');
+    return hashIndex >= 0 ? value.slice(0, hashIndex).trim() : value.trim();
+}
+function stripQuotes(value) {
+    const trimmed = stripInlineComment(value).trim();
+    if ((trimmed.startsWith('"') && trimmed.endsWith('"')) ||
+        (trimmed.startsWith("'") && trimmed.endsWith("'"))) {
+        return trimmed.slice(1, -1).trim();
+    }
+    return trimmed;
+}
+function parseArrayValue(value) {
+    const trimmed = stripInlineComment(value).trim();
+    if (!trimmed)
+        return [];
+    if (trimmed.startsWith('[') && trimmed.endsWith(']')) {
+        return trimmed
+            .slice(1, -1)
+            .split(',')
+            .map(item => stripQuotes(item))
+            .filter(Boolean);
+    }
+    return [stripQuotes(trimmed)].filter(Boolean);
+}
+function parseFrontmatter(content) {
+    if (!content.startsWith('---\n') && !content.startsWith('---\r\n')) {
+        return null;
+    }
+    const endMatch = content.match(/\r?\n---\r?\n/);
+    if (!endMatch || typeof endMatch.index !== 'number') {
+        return null;
+    }
+    const block = content.slice(content.indexOf('\n') + 1, endMatch.index);
+    const fields = {};
+    let currentListKey = null;
+    for (const rawLine of block.split(/\r?\n/)) {
+        const line = rawLine.trimEnd();
+        if (!line.trim() || line.trimStart().startsWith('#')) {
+            continue;
+        }
+        const listMatch = line.match(/^\s*-\s+(.+)$/);
+        if (listMatch && currentListKey) {
+            fields[currentListKey] = [...(fields[currentListKey] ?? []), ...parseArrayValue(listMatch[1])];
+            continue;
+        }
+        const fieldMatch = line.match(/^([A-Za-z0-9_.-]+):(?:\s*(.*))?$/);
+        if (!fieldMatch) {
+            currentListKey = null;
+            continue;
+        }
+        const key = fieldMatch[1];
+        const value = fieldMatch[2] ?? '';
+        currentListKey = value.trim() === '' ? key : null;
+        fields[key] = parseArrayValue(value);
+    }
+    return fields;
+}
+function first(fields, key) {
+    return fields[key]?.[0];
+}
+function getOwners(fields) {
+    return [...(fields.owners ?? []), ...(fields.owner ?? [])].filter(Boolean);
+}
+function toArtifact(projectDir, absPath, fields) {
+    const id = first(fields, 'id');
+    if (!id)
+        return null;
+    const relations = emptyRelations();
+    for (const field of RELATION_FIELDS) {
+        relations[field] = fields[field] ?? [];
+    }
+    return {
+        id,
+        file: normalizeRelPath(projectDir, absPath),
+        type: first(fields, 'type'),
+        status: first(fields, 'status'),
+        owners: getOwners(fields),
+        relations,
+    };
+}
+function targetFindingLevel(isExplicit) {
+    return isExplicit ? 'fail' : 'warn';
+}
+async function realpathOrNull(filePath) {
+    try {
+        return await fs.realpath(filePath);
+    }
+    catch {
+        return null;
+    }
+}
+async function collectMarkdownFiles(projectDir, targets, isExplicit) {
+    const canonicalProjectDir = await fs.realpath(projectDir);
+    const files = new Set();
+    const findings = [];
+    const visitedDirectories = new Set();
+    async function walk(currentPath, requestedPath, isRootTarget = false) {
+        const canonicalPath = await realpathOrNull(currentPath);
+        if (!canonicalPath) {
+            findings.push({
+                level: targetFindingLevel(isExplicit),
+                file: requestedPath,
+                message: `Requested audit target does not exist: ${requestedPath}`,
+            });
+            return;
+        }
+        if (!isInsideProject(canonicalProjectDir, canonicalPath)) {
+            findings.push({
+                level: targetFindingLevel(isExplicit),
+                file: requestedPath,
+                message: `Requested audit target is outside the project boundary: ${requestedPath}`,
+            });
+            return;
+        }
+        const stats = await fs.lstat(currentPath);
+        const statTarget = stats.isSymbolicLink() ? canonicalPath : currentPath;
+        const targetStats = stats.isSymbolicLink() ? await fs.stat(canonicalPath) : stats;
+        if (targetStats.isFile()) {
+            if (statTarget.endsWith('.md')) {
+                files.add(statTarget);
+            }
+            return;
+        }
+        if (!targetStats.isDirectory()) {
+            return;
+        }
+        if (visitedDirectories.has(canonicalPath)) {
+            return;
+        }
+        visitedDirectories.add(canonicalPath);
+        const directoryName = path.basename(currentPath);
+        if (!isRootTarget && DEFAULT_SKIP_DIRS.has(directoryName)) {
+            return;
+        }
+        const entries = await fs.readdir(canonicalPath, { withFileTypes: true });
+        entries.sort((a, b) => a.name.localeCompare(b.name));
+        for (const entry of entries) {
+            const entryPath = path.join(canonicalPath, entry.name);
+            const entryRequestedPath = path.join(requestedPath, entry.name).replaceAll('\\', '/');
+            await walk(entryPath, entryRequestedPath);
+        }
+    }
+    for (const target of targets) {
+        const absTarget = path.resolve(projectDir, target);
+        if (!isInsideProject(canonicalProjectDir, absTarget)) {
+            findings.push({
+                level: targetFindingLevel(isExplicit),
+                file: target,
+                message: `Requested audit target is outside the project boundary: ${target}`,
+            });
+            continue;
+        }
+        if (!await fs.pathExists(absTarget)) {
+            if (isExplicit) {
+                findings.push({
+                    level: 'fail',
+                    file: target,
+                    message: `Requested audit target does not exist: ${target}`,
+                });
+            }
+            continue;
+        }
+        await walk(absTarget, target, true);
+    }
+    return {
+        files: [...files].sort((a, b) => a.localeCompare(b)),
+        findings,
+    };
+}
+function relationTargets(artifact) {
+    return RELATION_FIELDS.flatMap(field => artifact.relations[field]);
+}
+function hasIncomingRelation(artifactId, artifacts, fields) {
+    return artifacts.some(artifact => fields.some(field => artifact.relations[field].includes(artifactId)));
+}
+function detectDependencyCycles(artifacts) {
+    const byId = new Map(artifacts.map(artifact => [artifact.id, artifact]));
+    const cycles = [];
+    const visiting = new Set();
+    const visited = new Set();
+    const stack = [];
+    function visit(id) {
+        if (visiting.has(id)) {
+            const start = stack.indexOf(id);
+            if (start >= 0) {
+                cycles.push([...stack.slice(start), id]);
+            }
+            return;
+        }
+        if (visited.has(id))
+            return;
+        const artifact = byId.get(id);
+        if (!artifact)
+            return;
+        visiting.add(id);
+        stack.push(id);
+        for (const targetId of artifact.relations.depends_on) {
+            visit(targetId);
+        }
+        stack.pop();
+        visiting.delete(id);
+        visited.add(id);
+    }
+    for (const artifact of artifacts) {
+        visit(artifact.id);
+    }
+    return cycles;
+}
+function auditRecords(artifacts, markdownWithoutMetadata) {
+    const findings = [];
+    const ids = new Map();
+    for (const artifact of artifacts) {
+        ids.set(artifact.id, [...(ids.get(artifact.id) ?? []), artifact]);
+    }
+    for (const [id, matches] of ids) {
+        if (matches.length > 1) {
+            findings.push({
+                level: 'fail',
+                id,
+                message: `Duplicate artifact id is used by ${matches.map(match => match.file).join(', ')}`,
+            });
+        }
+    }
+    const knownIds = new Set(ids.keys());
+    for (const artifact of artifacts) {
+        if (!artifact.type) {
+            findings.push({ level: 'warn', file: artifact.file, id: artifact.id, message: 'Missing type.' });
+        }
+        if (!artifact.status) {
+            findings.push({ level: 'warn', file: artifact.file, id: artifact.id, message: 'Missing status.' });
+        }
+        if (artifact.owners.length === 0) {
+            findings.push({ level: 'warn', file: artifact.file, id: artifact.id, message: 'Missing owner/owners.' });
+        }
+        for (const field of RELATION_FIELDS) {
+            for (const targetId of artifact.relations[field]) {
+                if (targetId === artifact.id) {
+                    findings.push({
+                        level: 'fail',
+                        file: artifact.file,
+                        id: artifact.id,
+                        message: `Self-reference in ${field}.`,
+                    });
+                }
+                else if (!knownIds.has(targetId)) {
+                    findings.push({
+                        level: 'fail',
+                        file: artifact.file,
+                        id: artifact.id,
+                        message: `${field} references unknown artifact "${targetId}".`,
+                    });
+                }
+            }
+        }
+        const type = artifact.type?.toLowerCase();
+        const status = artifact.status?.toLowerCase();
+        if ((type === 'spec' || type === 'requirement' || type === 'requirements') && relationTargets(artifact).length === 0) {
+            findings.push({
+                level: 'warn',
+                file: artifact.file,
+                id: artifact.id,
+                message: 'Spec has no explicit dependency/impact links.',
+            });
+        }
+        if ((type === 'spec' || type === 'requirement' || type === 'requirements') &&
+            !hasIncomingRelation(artifact.id, artifacts, ['implements', 'verifies', 'documents'])) {
+            findings.push({
+                level: 'warn',
+                file: artifact.file,
+                id: artifact.id,
+                message: 'Spec is not referenced by code/tests/docs metadata.',
+            });
+        }
+        if (type === 'adr' && status === 'accepted' && artifact.relations.affects.length === 0) {
+            findings.push({
+                level: 'warn',
+                file: artifact.file,
+                id: artifact.id,
+                message: 'Accepted ADR has no affects links.',
+            });
+        }
+    }
+    for (const cycle of detectDependencyCycles(artifacts)) {
+        findings.push({
+            level: 'fail',
+            message: `Dependency cycle: ${cycle.join(' -> ')}`,
+        });
+    }
+    if (markdownWithoutMetadata > 0 && artifacts.length === 0) {
+        findings.push({
+            level: 'warn',
+            message: `${markdownWithoutMetadata} markdown file(s) were found, but none had artifact frontmatter with an id.`,
+        });
+    }
+    return findings;
+}
+function printHumanReport(artifacts, findings, markdownWithoutMetadata, strict) {
+    const failCount = findings.filter(finding => finding.level === 'fail').length;
+    const warnCount = findings.filter(finding => finding.level === 'warn').length;
+    const effectiveFailCount = strict ? failCount + warnCount : failCount;
+    console.log(chalk.bold('Artifact Audit'));
+    console.log(`Artifacts indexed: ${artifacts.length}`);
+    console.log(`Markdown without artifact metadata: ${markdownWithoutMetadata}`);
+    console.log(`Findings: ${failCount} fail, ${warnCount} warn${strict ? ' (strict treats warnings as failures)' : ''}`);
+    console.log('');
+    if (findings.length === 0) {
+        console.log(chalk.green('PASS No artifact graph issues found.'));
+        return;
+    }
+    for (const finding of findings) {
+        const label = finding.level === 'fail' ? chalk.red('FAIL') : chalk.yellow('WARN');
+        const location = [finding.file, finding.id].filter(Boolean).join(' ');
+        console.log(`${label} ${location ? `${location}: ` : ''}${finding.message}`);
+    }
+    console.log('');
+    if (effectiveFailCount > 0) {
+        console.log(chalk.red('Result: FAIL'));
+    }
+    else {
+        console.log(chalk.yellow('Result: WARN'));
+    }
+}
+export async function auditArtifactsCommand(paths = [], options = {}) {
+    const projectDir = process.cwd();
+    const targets = paths.length > 0 ? paths : DEFAULT_TARGETS;
+    const explicitTargets = paths.length > 0;
+    const { files: markdownFiles, findings: collectionFindings } = await collectMarkdownFiles(projectDir, targets, explicitTargets);
+    const artifacts = [];
+    let markdownWithoutMetadata = 0;
+    for (const file of markdownFiles) {
+        const content = await readTextFile(file);
+        if (!content)
+            continue;
+        const fields = parseFrontmatter(content);
+        if (!fields) {
+            markdownWithoutMetadata += 1;
+            continue;
+        }
+        const artifact = toArtifact(projectDir, file, fields);
+        if (artifact) {
+            artifacts.push(artifact);
+        }
+        else {
+            markdownWithoutMetadata += 1;
+        }
+    }
+    const findings = [...collectionFindings, ...auditRecords(artifacts, markdownWithoutMetadata)];
+    const failCount = findings.filter(finding => finding.level === 'fail').length;
+    const warnCount = findings.filter(finding => finding.level === 'warn').length;
+    const shouldFail = options.strict ? failCount + warnCount > 0 : failCount > 0;
+    if (options.json) {
+        console.log(JSON.stringify({
+            status: shouldFail ? 'fail' : warnCount > 0 ? 'warn' : 'pass',
+            artifacts: artifacts.length,
+            markdown_without_metadata: markdownWithoutMetadata,
+            findings,
+        }, null, 2));
+    }
+    else {
+        printHumanReport(artifacts, findings, markdownWithoutMetadata, options.strict ?? false);
+    }
+    if (shouldFail) {
+        process.exitCode = 1;
+    }
+}
+//# sourceMappingURL=audit-artifacts.js.map

package/dist/cli/commands/audit-artifacts.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"extension.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/extension.ts"],"names":[],"mappings":"AA4CA,wBAAsB,mBAAmB,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CA6CvE;AAED,wBAAsB,sBAAsB,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAkFxE;AAED,wBAAsB,oBAAoB,IAAI,OAAO,CAAC,IAAI,CAAC,CAoC1D;AAED,wBAAsB,sBAAsB,CAAC,IAAI,CAAC,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE;IAAE,KAAK,CAAC,EAAE,OAAO,CAAA;CAAE,GAAG,OAAO,CAAC,IAAI,CAAC,CAkFxG"}
+{"version":3,"file":"extension.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/extension.ts"],"names":[],"mappings":"AAkDA,wBAAsB,mBAAmB,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CA6CvE;AAED,wBAAsB,sBAAsB,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CA4FxE;AAED,wBAAsB,oBAAoB,IAAI,OAAO,CAAC,IAAI,CAAC,CAoC1D;AAED,wBAAsB,sBAAsB,CAAC,IAAI,CAAC,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE;IAAE,KAAK,CAAC,EAAE,OAAO,CAAA;CAAE,GAAG,OAAO,CAAC,IAAI,CAAC,CAkFxG"}

package/dist/cli/commands/extension.js

@@ -1,10 +1,10 @@
 import chalk from 'chalk';
 import path from 'path';
-import { loadConfig, saveConfig } from '../../core/config.js';
+import { hydrateAgentFileSources, loadConfig, saveConfig } from '../../core/config.js';
 import { hydrateProjectAgentRegistry } from '../../core/agents.js';
-import { resolveExtension, removeExtensionFiles, getExtensionsDir, loadExtensionManifest, } from '../../core/extensions.js';
+import { resolveExtension, removeExtensionFiles, getExtensionsDir, loadInstalledExtensionManifest, } from '../../core/extensions.js';
 import { removeExtensionMcpServers } from '../../core/mcp.js';
-import { removeSkillsForAllAgents, collectReplacedSkills, removeExtensionAgentFilesForAllAgents, restoreBaseSkills, stripInjectionsForAllAgents, removeCustomSkillsForAllAgents, commitResolvedExtension, refreshExtensions, getManifestRuntimeIds, assertNoConfiguredRuntimeOrphans, } from '../../core/extension-ops.js';
+import { collectTrackedExtensionAgentFileTargets, removeSkillsForAllAgents, collectReplacedSkills, collectManifestAgentFileTargets, removeAgentFilesForAllAgentsByTargets, removeExtensionAgentFilesForAllAgents, pruneAgentFileSources, pruneInstalledAgentFiles, pruneManagedAgentFiles, restoreBaseSkills, stripInjectionsForAllAgents, removeCustomSkillsForAllAgents, commitResolvedExtension, refreshExtensions, getManifestRuntimeIds, assertNoConfiguredRuntimeOrphans, } from '../../core/extension-ops.js';
 async function loadHydratedExtensionConfig(projectDir, options = {}) {
     const config = await loadConfig(projectDir);
     if (!config) {
@@ -66,6 +66,7 @@ export async function extensionRemoveCommand(name) {
     const projectDir = process.cwd();
     console.log(chalk.bold.blue('\n🏭 AI Factory - Remove Extension\n'));
     const config = await loadHydratedExtensionConfig(projectDir);
+    await hydrateAgentFileSources(projectDir, config);
     const extensions = config.extensions ?? [];
     const index = extensions.findIndex(e => e.name === name);
     if (index < 0) {
@@ -74,10 +75,18 @@ export async function extensionRemoveCommand(name) {
     }
     try {
         const extensionDir = path.join(getExtensionsDir(projectDir), name);
-        const manifest = await loadExtensionManifest(extensionDir);
+        const manifest = await loadInstalledExtensionManifest(extensionDir);
         assertNoConfiguredRuntimeOrphans(config, getManifestRuntimeIds(manifest), name, 'remove');
-        if (manifest?.agentFiles?.length) {
-            const removedAgentFiles = await removeExtensionAgentFilesForAllAgents(projectDir, config.agents, manifest);
+        const trackedAgentFileTargets = manifest?.agentFiles?.length
+            ? collectManifestAgentFileTargets(manifest)
+            : collectTrackedExtensionAgentFileTargets(config.agents, name);
+        if (Array.from(trackedAgentFileTargets.values()).some(targets => targets.length > 0)) {
+            const removedAgentFiles = manifest?.agentFiles?.length
+                ? await removeExtensionAgentFilesForAllAgents(projectDir, config.agents, manifest)
+                : await removeAgentFilesForAllAgentsByTargets(projectDir, config.agents, trackedAgentFileTargets);
+            pruneInstalledAgentFiles(config.agents, trackedAgentFileTargets);
+            pruneAgentFileSources(config.agents, trackedAgentFileTargets);
+            pruneManagedAgentFiles(config.agents, trackedAgentFileTargets);
             for (const [agentId, files] of removedAgentFiles) {
                 if (files.length > 0) {
                     console.log(chalk.green(`✓ Agent files removed for ${agentId}: ${files.join(', ')}`));
@@ -145,7 +154,7 @@ export async function extensionListCommand() {
         console.log(`  ${chalk.bold(ext.name)} ${chalk.dim(`v${ext.version}`)}`);
         console.log(chalk.dim(`    Source: ${ext.source}`));
         const extensionDir = path.join(getExtensionsDir(projectDir), ext.name);
-        const manifest = await loadExtensionManifest(extensionDir);
+        const manifest = await loadInstalledExtensionManifest(extensionDir);
         if (manifest) {
             if (manifest.description) {
                 console.log(chalk.dim(`    ${manifest.description}`));