@cubis/foundry 0.3.34 → 0.3.36

package/workflows/workflows/agent-environment-setup/platforms/windsurf/skills/atlassian-mcp/SKILL.md

@@ -1,88 +0,0 @@
----
-name: atlassian-mcp
-description: Use when querying Jira issues, searching Confluence pages, creating tickets, updating documentation, or integrating Atlassian tools via MCP protocol.
-license: MIT
-metadata:
-  author: https://github.com/Jeffallan
-  version: "1.0.0"
-  domain: platform
-  triggers: Jira, Confluence, Atlassian, MCP, tickets, issues, wiki, JQL, CQL, sprint, backlog, project management
-  role: expert
-  scope: implementation
-  output-format: code
-  related-skills: mcp-developer, api-designer, security-reviewer
----
-
-# Atlassian MCP Expert
-
-Senior integration specialist with deep expertise in connecting Jira, Confluence, and other Atlassian tools to AI systems via Model Context Protocol (MCP).
-
-## Role Definition
-
-You are an expert in Atlassian MCP integration with mastery of both official and open-source MCP servers, JQL/CQL query languages, OAuth 2.0 authentication, and production deployment patterns. You build robust workflows that automate issue triage, documentation sync, sprint planning, and cross-tool integration while respecting permissions and maintaining security.
-
-## When to Use This Skill
-
-- Querying Jira issues with JQL filters
-- Searching or creating Confluence pages
-- Automating sprint workflows and backlog management
-- Setting up MCP server authentication (OAuth/API tokens)
-- Syncing meeting notes to Jira tickets
-- Generating documentation from issue data
-- Debugging Atlassian API integration issues
-- Choosing between official vs open-source MCP servers
-
-## Core Workflow
-
-1. **Select server** - Choose official cloud, open-source, or self-hosted MCP server
-2. **Authenticate** - Configure OAuth 2.1, API tokens, or PAT credentials
-3. **Design queries** - Write JQL for Jira, CQL for Confluence, test filters
-4. **Implement workflow** - Build tool calls, handle pagination, error recovery
-5. **Deploy** - Configure IDE integration, test permissions, monitor rate limits
-
-## Reference Guide
-
-Load detailed guidance based on context:
-
-| Topic | Reference | Load When |
-|-------|-----------|-----------|
-| Server Setup | `references/mcp-server-setup.md` | Installation, choosing servers, configuration |
-| Jira Operations | `references/jira-queries.md` | JQL syntax, issue CRUD, sprints, boards |
-| Confluence Ops | `references/confluence-operations.md` | CQL search, page creation, spaces, comments |
-| Authentication | `references/authentication-patterns.md` | OAuth 2.0, API tokens, permission scopes |
-| Common Workflows | `references/common-workflows.md` | Issue triage, doc sync, sprint automation |
-
-## Constraints
-
-### MUST DO
-- Respect user permissions and workspace access controls
-- Validate JQL/CQL queries before execution
-- Handle rate limits with exponential backoff
-- Use pagination for large result sets (50-100 items per page)
-- Implement error recovery for network failures
-- Log API calls for debugging and audit trails
-- Test with read-only operations first
-- Document required permission scopes
-
-### MUST NOT DO
-- Hardcode API tokens or OAuth secrets in code
-- Ignore rate limit headers from Atlassian APIs
-- Create issues without validating required fields
-- Skip input sanitization on user-provided query strings
-- Deploy without testing permission boundaries
-- Update production data without confirmation prompts
-- Mix different authentication methods in same session
-- Expose sensitive issue data in logs or error messages
-
-## Output Templates
-
-When implementing Atlassian MCP features, provide:
-1. MCP server configuration (JSON/environment vars)
-2. Query examples (JQL/CQL with explanations)
-3. Tool call implementation with error handling
-4. Authentication setup instructions
-5. Brief explanation of permission requirements
-
-## Knowledge Reference
-
-Atlassian MCP Server (official), mcp-atlassian (sooperset), atlassian-mcp (xuanxt), JQL (Jira Query Language), CQL (Confluence Query Language), OAuth 2.1, API tokens, Personal Access Tokens (PAT), Model Context Protocol, JSON-RPC 2.0, rate limiting, pagination, permission scopes, Jira REST API, Confluence REST API

package/workflows/workflows/agent-environment-setup/platforms/windsurf/skills/atlassian-mcp/references/authentication-patterns.md

@@ -1,520 +0,0 @@
-# Authentication Patterns
-
----
-
-## Authentication Methods Overview
-
-| Method | Platform | Use Case | Security Level |
-|--------|----------|----------|----------------|
-| OAuth 2.1 | Cloud | User-facing apps, integrations | Highest |
-| API Token | Cloud | Personal automation, scripts | Medium |
-| PAT | Server/DC | Server integrations | Medium |
-| Basic Auth | Legacy | Deprecated, avoid | Low |
-
-## OAuth 2.1 (Atlassian Cloud)
-
-### Authorization Code Flow
-
-For applications that act on behalf of users.
-
-**Step 1: Register Your App**
-
-1. Go to [developer.atlassian.com](https://developer.atlassian.com/console/myapps/)
-2. Create new app
-3. Configure OAuth 2.0 (3LO)
-4. Add callback URL
-5. Request necessary scopes
-
-**Step 2: Authorization Request**
-
-```typescript
-const authUrl = new URL('https://auth.atlassian.com/authorize');
-authUrl.searchParams.set('audience', 'api.atlassian.com');
-authUrl.searchParams.set('client_id', CLIENT_ID);
-authUrl.searchParams.set('scope', 'read:jira-work write:jira-work read:confluence-content.all write:confluence-content');
-authUrl.searchParams.set('redirect_uri', REDIRECT_URI);
-authUrl.searchParams.set('state', generateState());
-authUrl.searchParams.set('response_type', 'code');
-authUrl.searchParams.set('prompt', 'consent');
-
-// Redirect user to authUrl.toString()
-```
-
-**Step 3: Exchange Code for Token**
-
-```typescript
-async function exchangeCodeForToken(code: string): Promise<TokenResponse> {
-  const response = await fetch('https://auth.atlassian.com/oauth/token', {
-    method: 'POST',
-    headers: {
-      'Content-Type': 'application/json',
-    },
-    body: JSON.stringify({
-      grant_type: 'authorization_code',
-      client_id: CLIENT_ID,
-      client_secret: CLIENT_SECRET,
-      code,
-      redirect_uri: REDIRECT_URI,
-    }),
-  });
-
-  if (!response.ok) {
-    throw new Error(`Token exchange failed: ${response.statusText}`);
-  }
-
-  return response.json();
-}
-
-interface TokenResponse {
-  access_token: string;
-  refresh_token: string;
-  expires_in: number;
-  scope: string;
-  token_type: 'Bearer';
-}
-```
-
-**Step 4: Refresh Token**
-
-```typescript
-async function refreshAccessToken(refreshToken: string): Promise<TokenResponse> {
-  const response = await fetch('https://auth.atlassian.com/oauth/token', {
-    method: 'POST',
-    headers: {
-      'Content-Type': 'application/json',
-    },
-    body: JSON.stringify({
-      grant_type: 'refresh_token',
-      client_id: CLIENT_ID,
-      client_secret: CLIENT_SECRET,
-      refresh_token: refreshToken,
-    }),
-  });
-
-  return response.json();
-}
-```
-
-**Step 5: Get Accessible Resources**
-
-```typescript
-async function getAccessibleResources(accessToken: string): Promise<Resource[]> {
-  const response = await fetch(
-    'https://api.atlassian.com/oauth/token/accessible-resources',
-    {
-      headers: {
-        Authorization: `Bearer ${accessToken}`,
-        Accept: 'application/json',
-      },
-    }
-  );
-
-  return response.json();
-}
-
-interface Resource {
-  id: string;        // Cloud ID
-  name: string;      // Site name
-  url: string;       // https://your-site.atlassian.net
-  scopes: string[];
-  avatarUrl: string;
-}
-```
-
-### OAuth Scopes Reference
-
-**Jira Scopes:**
-
-| Scope | Description |
-|-------|-------------|
-| `read:jira-work` | Read issues, projects, boards |
-| `write:jira-work` | Create/update issues |
-| `manage:jira-project` | Manage project settings |
-| `manage:jira-configuration` | Manage global settings |
-| `read:jira-user` | Read user profiles |
-| `manage:jira-data-provider` | Data provider integrations |
-
-**Confluence Scopes:**
-
-| Scope | Description |
-|-------|-------------|
-| `read:confluence-content.all` | Read all content |
-| `write:confluence-content` | Create/update content |
-| `read:confluence-content.summary` | Read content summaries |
-| `read:confluence-space.summary` | Read space summaries |
-| `write:confluence-space` | Create/manage spaces |
-| `read:confluence-user` | Read user profiles |
-
-**Granular Scopes (v2):**
-
-```
-read:issue-details:jira
-write:issue:jira
-read:sprint:jira-software
-write:sprint:jira-software
-read:page:confluence
-write:page:confluence
-read:comment:confluence
-write:comment:confluence
-```
-
-## API Tokens (Atlassian Cloud)
-
-### Creating API Token
-
-1. Go to [id.atlassian.com/manage-profile/security/api-tokens](https://id.atlassian.com/manage-profile/security/api-tokens)
-2. Click "Create API token"
-3. Give it a descriptive label
-4. Copy token immediately (shown only once)
-
-### Using API Token
-
-```typescript
-// Basic authentication with API token
-const credentials = Buffer.from(`${email}:${apiToken}`).toString('base64');
-
-const response = await fetch('https://your-site.atlassian.net/rest/api/3/myself', {
-  headers: {
-    Authorization: `Basic ${credentials}`,
-    Accept: 'application/json',
-  },
-});
-
-// For MCP server configuration
-const config = {
-  JIRA_URL: 'https://your-site.atlassian.net',
-  JIRA_USERNAME: 'your-email@company.com',
-  JIRA_API_TOKEN: 'your-api-token',
-};
-```
-
-### Token Security Best Practices
-
-```typescript
-// Store tokens securely
-import { SecretManagerServiceClient } from '@google-cloud/secret-manager';
-import { SecretsManager } from '@aws-sdk/client-secrets-manager';
-
-// Option 1: Environment variables (development only)
-const token = process.env.ATLASSIAN_API_TOKEN;
-
-// Option 2: GCP Secret Manager
-async function getTokenFromGCP(secretName: string): Promise<string> {
-  const client = new SecretManagerServiceClient();
-  const [version] = await client.accessSecretVersion({
-    name: `projects/my-project/secrets/${secretName}/versions/latest`,
-  });
-  return version.payload?.data?.toString() || '';
-}
-
-// Option 3: AWS Secrets Manager
-async function getTokenFromAWS(secretName: string): Promise<string> {
-  const client = new SecretsManager({ region: 'us-east-1' });
-  const response = await client.getSecretValue({ SecretId: secretName });
-  return response.SecretString || '';
-}
-
-// Option 4: HashiCorp Vault
-async function getTokenFromVault(path: string): Promise<string> {
-  const response = await fetch(`${VAULT_ADDR}/v1/${path}`, {
-    headers: { 'X-Vault-Token': VAULT_TOKEN },
-  });
-  const data = await response.json();
-  return data.data.data.token;
-}
-```
-
-## Personal Access Tokens (Server/Data Center)
-
-### Creating PAT
-
-**Jira Server/DC:**
-1. Profile > Personal Access Tokens
-2. Create token
-3. Set expiration date
-4. Select permissions
-
-**Confluence Server/DC:**
-1. Profile > Settings > Personal Access Tokens
-2. Create token
-3. Configure permissions
-
-### Using PAT
-
-```typescript
-// Bearer token authentication
-const response = await fetch('https://jira.internal.company.com/rest/api/2/myself', {
-  headers: {
-    Authorization: `Bearer ${personalAccessToken}`,
-    Accept: 'application/json',
-  },
-});
-
-// MCP server configuration
-const config = {
-  JIRA_URL: 'https://jira.internal.company.com',
-  JIRA_PERSONAL_TOKEN: 'your-personal-access-token',
-};
-```
-
-### PAT Permissions
-
-| Permission | Jira | Confluence |
-|------------|------|------------|
-| Read | Browse projects, view issues | View pages |
-| Write | Create/edit issues | Create/edit pages |
-| Admin | Project administration | Space administration |
-
-## Token Management
-
-### Token Lifecycle Manager
-
-```typescript
-interface TokenInfo {
-  accessToken: string;
-  refreshToken?: string;
-  expiresAt: Date;
-  scopes: string[];
-}
-
-class TokenManager {
-  private tokenInfo: TokenInfo | null = null;
-  private refreshThreshold = 5 * 60 * 1000; // 5 minutes
-
-  async getValidToken(): Promise<string> {
-    if (!this.tokenInfo) {
-      throw new Error('Not authenticated');
-    }
-
-    // Check if token needs refresh
-    const timeUntilExpiry = this.tokenInfo.expiresAt.getTime() - Date.now();
-
-    if (timeUntilExpiry < this.refreshThreshold) {
-      await this.refreshToken();
-    }
-
-    return this.tokenInfo.accessToken;
-  }
-
-  private async refreshToken(): Promise<void> {
-    if (!this.tokenInfo?.refreshToken) {
-      throw new Error('No refresh token available');
-    }
-
-    const response = await refreshAccessToken(this.tokenInfo.refreshToken);
-
-    this.tokenInfo = {
-      accessToken: response.access_token,
-      refreshToken: response.refresh_token || this.tokenInfo.refreshToken,
-      expiresAt: new Date(Date.now() + response.expires_in * 1000),
-      scopes: response.scope.split(' '),
-    };
-  }
-
-  isAuthenticated(): boolean {
-    return this.tokenInfo !== null && this.tokenInfo.expiresAt > new Date();
-  }
-
-  getScopes(): string[] {
-    return this.tokenInfo?.scopes || [];
-  }
-
-  hasScope(scope: string): boolean {
-    return this.getScopes().includes(scope);
-  }
-}
-```
-
-### Token Rotation Strategy
-
-```typescript
-class TokenRotationManager {
-  private rotationInterval = 30 * 24 * 60 * 60 * 1000; // 30 days
-
-  async checkAndRotate(tokenCreatedAt: Date): Promise<boolean> {
-    const age = Date.now() - tokenCreatedAt.getTime();
-
-    if (age > this.rotationInterval) {
-      console.warn('API token is due for rotation');
-      return true;
-    }
-
-    return false;
-  }
-
-  async sendRotationReminder(email: string, tokenLabel: string): Promise<void> {
-    // Integrate with your notification system
-    await sendEmail({
-      to: email,
-      subject: 'Atlassian API Token Rotation Reminder',
-      body: `Your API token "${tokenLabel}" is due for rotation.
-             Please create a new token and update your integrations.`,
-    });
-  }
-}
-```
-
-## Permission Verification
-
-### Check Current Permissions
-
-```typescript
-async function verifyPermissions(
-  client: MCPClient,
-  requiredOperations: string[]
-): Promise<PermissionReport> {
-  const report: PermissionReport = {
-    hasAllPermissions: true,
-    details: [],
-  };
-
-  for (const operation of requiredOperations) {
-    try {
-      switch (operation) {
-        case 'read:jira':
-          await client.callTool({
-            name: 'jira_get_issue',
-            arguments: { issue_key: 'TEST-1' },
-          });
-          break;
-        case 'write:jira':
-          // Create and immediately delete a test issue
-          const created = await client.callTool({
-            name: 'jira_create_issue',
-            arguments: {
-              project_key: 'TEST',
-              issue_type: 'Task',
-              summary: '[Permission Test] Delete me',
-            },
-          });
-          // Clean up
-          await client.callTool({
-            name: 'jira_delete_issue',
-            arguments: { issue_key: JSON.parse(created.content[0].text).key },
-          });
-          break;
-        case 'read:confluence':
-          await client.callTool({
-            name: 'confluence_search',
-            arguments: { cql: 'type = page', limit: 1 },
-          });
-          break;
-      }
-
-      report.details.push({ operation, status: 'granted' });
-    } catch (error: any) {
-      report.hasAllPermissions = false;
-      report.details.push({
-        operation,
-        status: 'denied',
-        error: error.message,
-      });
-    }
-  }
-
-  return report;
-}
-```
-
-## Security Checklist
-
-### Do:
-- Use OAuth 2.1 for user-facing applications
-- Store secrets in dedicated secrets management systems
-- Implement token rotation policies
-- Use minimal required scopes
-- Log authentication events (without secrets)
-- Implement rate limiting at application level
-- Validate tokens before use
-
-### Don't:
-- Hardcode tokens in source code
-- Log tokens or secrets
-- Share tokens between environments
-- Use Basic Auth (deprecated)
-- Request more scopes than needed
-- Store tokens in browser localStorage
-- Commit `.env` files with real credentials
-
-### Environment Configuration Template
-
-```bash
-# .env.example (commit this)
-ATLASSIAN_SITE_URL=https://your-site.atlassian.net
-ATLASSIAN_AUTH_TYPE=oauth  # or 'api_token' or 'pat'
-
-# OAuth settings (if using OAuth)
-ATLASSIAN_CLIENT_ID=
-ATLASSIAN_CLIENT_SECRET=
-
-# API Token settings (if using API token)
-ATLASSIAN_USERNAME=
-ATLASSIAN_API_TOKEN=
-
-# PAT settings (if using Server/DC)
-ATLASSIAN_PERSONAL_TOKEN=
-```
-
-```bash
-# .gitignore
-.env
-.env.local
-.env.*.local
-credentials.json
-**/secrets/**
-```
-
-## Troubleshooting
-
-### Common Authentication Errors
-
-**401 Unauthorized:**
-- Invalid or expired token
-- Wrong authentication method
-- Missing Authorization header
-
-**403 Forbidden:**
-- Token valid but lacks required scope
-- Resource-level permission denied
-- IP allowlist blocking request
-
-**Token refresh fails:**
-- Refresh token expired (after 90 days of inactivity)
-- Client secret changed
-- App permissions revoked
-
-### Debug Authentication
-
-```typescript
-async function debugAuth(token: string): Promise<void> {
-  // Check token validity
-  const meResponse = await fetch(
-    'https://api.atlassian.com/me',
-    { headers: { Authorization: `Bearer ${token}` } }
-  );
-
-  console.log('Token status:', meResponse.status);
-
-  if (meResponse.ok) {
-    const me = await meResponse.json();
-    console.log('Authenticated as:', me.email);
-  }
-
-  // Check accessible resources
-  const resourcesResponse = await fetch(
-    'https://api.atlassian.com/oauth/token/accessible-resources',
-    { headers: { Authorization: `Bearer ${token}` } }
-  );
-
-  if (resourcesResponse.ok) {
-    const resources = await resourcesResponse.json();
-    console.log('Accessible sites:', resources.map((r: any) => r.name));
-  }
-}
-```
-
-## Related References
-
-- `mcp-server-setup.md` - Server configuration with credentials
-- `jira-queries.md` - Operations that require authentication
-- `confluence-operations.md` - Content operations with auth