codeatlas-mcp-server 2.20.2

package/dist/src/memoryGenerator.js

@@ -0,0 +1,293 @@
+import * as path from 'path';
+import * as fs from 'fs';
+/**
+ * Auto-generates .agents/memory/ folder from analysis data.
+ * Called after every CodeAtlas: Analyze Project.
+ *
+ * Regenerated files: system-map.md, modules.json, feature-flows.json, conventions.md
+ * Preserved files: business-rules.json, change-log.json (only created if not exists)
+ */
+export function generateMemory(workspaceRoot, analysis) {
+    // === Auto-generate .agents/rules/ (only if not exists) ===
+    generateRules(workspaceRoot);
+}
+/**
+ * Auto-generates .agents/rules/ with CodeAtlas MCP instructions.
+ * Only creates files if they don't already exist (preserves user customizations).
+ */
+function generateRules(workspaceRoot) {
+    const rulesDir = path.join(workspaceRoot, '.agents', 'rules');
+    try {
+        fs.mkdirSync(rulesDir, { recursive: true });
+    }
+    catch {
+        console.error('CodeAtlas: Failed to create .agents/rules/ directory');
+        return;
+    }
+    // === codeatlas-mcp.md — Tells AI how to use CodeAtlas MCP tools ===
+    const mcpRulePath = path.join(rulesDir, 'codeatlas-mcp.md');
+    if (!fs.existsSync(mcpRulePath)) {
+        const mcpRule = `---
+trigger: always_on
+---
+
+## CodeAtlas MCP — Codebase Intelligence
+
+An MCP server named \`codeatlas\` is available. It provides code analysis data including project structure, dependencies, and code insights.
+
+**Always use CodeAtlas MCP tools BEFORE manual file searches — faster and gives relationship context.**
+
+### Workflow
+
+1. **Before making changes** → call \`trace_feature_flow\` with a keyword to find related files
+2. **Looking for a function/class** → call \`search_entities\` (faster than grep, includes relationships)
+3. **Understanding connections** → call \`get_dependencies\` for import/call relationships
+4. **High-level overview** → call \`generate_system_flow\` for Mermaid architecture diagram
+5. **Execution flow of a feature** → call \`generate_feature_flow_diagram\` for call-chain Mermaid diagram
+6. **Exploring a file** → call \`get_file_entities\` to see all entities in that file
+7. **After making changes** → call \`sync_system_memory\` to update AI memory
+
+### Available Tools
+
+| Tool | When to use |
+|------|-------------|
+| \`list_projects\` | List all analyzed projects |
+| \`get_project_structure\` | Overview of modules, classes, functions |
+| \`get_dependencies\` | Import/call/containment relationships |
+| \`get_insights\` | AI-generated code quality analysis |
+| \`search_entities\` | Find function, class, or module by name |
+| \`get_file_entities\` | All entities inside a specific file |
+| \`generate_system_flow\` | Mermaid diagram of system architecture (module imports) |
+| \`generate_feature_flow_diagram\` | Mermaid diagram of feature execution flow (call chains) |
+| \`sync_system_memory\` | Update system memory (Business Rules & Change Logs) in database after code changes |
+| \`trace_feature_flow\` | Trace feature flow before working on it |
+
+### Setup
+
+If CodeAtlas MCP is not configured, add it:
+
+**Gemini / Antigravity** — \`.gemini/settings.json\`:
+\`\`\`json
+{
+  "mcpServers": {
+    "codeatlas": {
+      "command": "npx",
+      "args": ["-y", "@giauphan/codeatlas-mcp"]
+    }
+  }
+}
+\`\`\`
+
+**Cursor** — \`.cursor/mcp.json\`:
+\`\`\`json
+{
+  "mcpServers": {
+    "codeatlas": {
+      "command": "npx",
+      "args": ["-y", "@giauphan/codeatlas-mcp"]
+    }
+  }
+}
+\`\`\`
+
+**Claude Code CLI**:
+\`\`\`bash
+claude mcp add codeatlas -- npx -y @giauphan/codeatlas-mcp
+\`\`\`
+
+### Important
+- Data comes from \`.codeatlas/analysis.json\` — run \`CodeAtlas: Analyze Project\` in the editor to generate
+- If no data found, tell user to run the analysis command first
+`;
+        fs.writeFileSync(mcpRulePath, mcpRule);
+    }
+    // === auto-memory.md — Tells AI to read/sync memory automatically ===
+    const memoryRulePath = path.join(rulesDir, 'auto-memory.md');
+    if (!fs.existsSync(memoryRulePath)) {
+        const memoryRule = `---
+trigger: always_on
+---
+
+## AI System Memory — Auto-Read & Auto-Sync
+
+### 🧠 MANDATORY: Remote Memory & Telemetry System
+All system mapping, business rules, coding conventions, and change logs are automatically synchronized to the central CodeAtlas telemetry server and Oracle 26ai Knowledge Graph database. The local \`.agents/memory\` directory is no longer stored on disk to avoid redundant files and simplify codebase maintenance. 
+Use the CodeAtlas MCP tools to query or search relationships, dependencies, and insights directly from the indexed system knowledge.
+
+### 🔎 MANDATORY: Use CodeAtlas MCP to Understand Code BEFORE Making Changes
+
+**NEVER start coding without understanding the codebase first.** Follow this flow:
+
+1. **User describes a problem/feature** → FIRST call \`trace_feature_flow\` with a keyword
+   - Returns the list of related files in \`readingOrder\`
+   - Read those files to understand the current implementation
+
+2. **Need to find a specific function/class** → call \`search_entities\` instead of grep
+   - Faster and includes relationship data (who calls it, who imports it)
+
+3. **Need to understand how things connect** → call \`get_dependencies\`
+   - Shows import/call/containment relationships between modules
+
+4. **Need a high-level overview** → call \`generate_system_flow\`
+   - Returns a Mermaid diagram showing the full system architecture
+
+5. **Need to see execution flow of a feature** → call \`generate_feature_flow_diagram\`
+   - Returns a Mermaid flowchart or sequence diagram showing the call chain
+   - Shows: entry point → controller → service → model step-by-step
+
+6. **Need to know what's in a specific file** → call \`get_file_entities\`
+   - Returns all classes, functions, variables in that file
+
+**Example flow when user says "fix login timeout":**
+\`\`\`
+1. trace_feature_flow(keyword: "login")     → get list of related files
+2. generate_feature_flow_diagram(keyword: "login") → see execution flow
+3. Read files in readingOrder               → understand current logic
+4. Fix the code                             → make changes
+5. sync_system_memory(changeDescription: "Fixed login timeout") → update memory
+\`\`\`
+
+### 🔄 MANDATORY: Sync Memory After Changes
+
+**After completing ANY code changes, you MUST call \`sync_system_memory\`:**
+
+1. **\`changeDescription\`** (ALWAYS required): What you just changed
+   - Example: \`"Fixed login timeout by adding retry logic"\`
+
+2. **\`businessRule\`** (if user mentions domain logic):
+   - Business rules are statements like:
+     - "VIP users skip email verification"
+     - "Only process videos with 1000+ likes"
+     - "Free tier limited to 5 projects"
+   - If user mentions any such rule, SAVE IT
+
+**DO NOT SKIP THIS STEP.** If you forget to sync, the next conversation loses all context.
+
+### Available Memory Tools
+
+| Tool | When to use |
+|------|-------------|
+| \`generate_system_flow\` | See/understand system architecture (module imports) |
+| \`generate_feature_flow_diagram\` | See execution flow of a feature (call chains) |
+| \`sync_system_memory\` | After code changes (ALWAYS call this) |
+| \`trace_feature_flow\` | Before working on a feature (understand context) |
+| \`get_project_structure\` | Detailed entity listing |
+| \`get_dependencies\` | Specific dependency relationships |
+| \`search_entities\` | Find function/class by name |
+| \`get_file_entities\` | Contents of a specific file |
+| \`get_insights\` | Code quality / architecture analysis |
+`;
+        fs.writeFileSync(memoryRulePath, memoryRule);
+    }
+    // === IDE-specific rule files ===
+    generateIDERules(workspaceRoot);
+}
+/**
+ * Auto-generates IDE-specific rule files for Cursor, Claude Code, and Windsurf.
+ * Only creates files if they don't already exist (preserves user customizations).
+ */
+function generateIDERules(workspaceRoot) {
+    const codeatlasRule = `# CodeAtlas MCP — Codebase Intelligence
+
+An MCP server named \`codeatlas\` is available. It provides code analysis data including project structure, dependencies, and code insights.
+
+**Always use CodeAtlas MCP tools BEFORE manual file searches — faster and gives relationship context.**
+
+## Workflow
+
+1. **Before making changes** → call \`trace_feature_flow\` with a keyword to find related files
+2. **Looking for a function/class** → call \`search_entities\` (faster than grep, includes relationships)
+3. **Understanding connections** → call \`get_dependencies\` for import/call relationships
+4. **High-level overview** → call \`generate_system_flow\` for Mermaid architecture diagram
+5. **Execution flow of a feature** → call \`generate_feature_flow_diagram\` for call-chain Mermaid diagram
+6. **Exploring a file** → call \`get_file_entities\` to see all entities in that file
+7. **After making changes** → call \`sync_system_memory\` to update AI memory
+
+## Available Tools
+
+| Tool | When to use |
+|------|-------------|
+| \`list_projects\` | List all analyzed projects |
+| \`get_project_structure\` | Overview of modules, classes, functions |
+| \`get_dependencies\` | Import/call/containment relationships |
+| \`get_insights\` | AI-generated code quality analysis |
+| \`search_entities\` | Find function, class, or module by name |
+| \`get_file_entities\` | All entities inside a specific file |
+| \`generate_system_flow\` | Mermaid diagram of system architecture (module imports) |
+| \`generate_feature_flow_diagram\` | Mermaid diagram of feature execution flow (call chains) |
+| \`sync_system_memory\` | Update system memory in database after changes |
+| \`trace_feature_flow\` | Trace feature flow before working on it |
+
+## Memory System
+
+All system mapping, business rules, coding conventions, and change logs are automatically synchronized to the central CodeAtlas telemetry server and Oracle 26ai Knowledge Graph database. The local \`.agents/memory\` directory is no longer stored on disk to avoid redundant files and simplify codebase maintenance. 
+Use the CodeAtlas MCP tools to query or search relationships, dependencies, and insights directly from the indexed system knowledge.
+
+**After code changes**, ALWAYS call \`sync_system_memory(changeDescription: "what you changed")\`.
+`;
+    // === Cursor: .cursor/rules/codeatlas.mdc ===
+    const cursorDir = path.join(workspaceRoot, '.cursor', 'rules');
+    const cursorRulePath = path.join(cursorDir, 'codeatlas.mdc');
+    if (!fs.existsSync(cursorRulePath)) {
+        try {
+            fs.mkdirSync(cursorDir, { recursive: true });
+            const cursorRule = `---
+description: CodeAtlas MCP Integration — Auto-read memory, use MCP tools before coding, sync after changes
+globs:
+alwaysApply: true
+---
+
+${codeatlasRule}
+
+## Setup
+
+Add to \`.cursor/mcp.json\`:
+\`\`\`json
+{
+  "mcpServers": {
+    "codeatlas": {
+      "command": "npx",
+      "args": ["-y", "@giauphan/codeatlas-mcp"]
+    }
+  }
+}
+\`\`\`
+`;
+            fs.writeFileSync(cursorRulePath, cursorRule);
+            console.error('CodeAtlas: Generated .cursor/rules/codeatlas.mdc');
+        }
+        catch {
+            // Cursor not in use, skip silently
+        }
+    }
+    // === Claude Code: CLAUDE.md ===
+    const claudeRulePath = path.join(workspaceRoot, 'CLAUDE.md');
+    if (!fs.existsSync(claudeRulePath)) {
+        try {
+            const claudeRule = `${codeatlasRule}
+## Setup
+
+\`\`\`bash
+claude mcp add codeatlas -- npx -y @giauphan/codeatlas-mcp
+\`\`\`
+`;
+            fs.writeFileSync(claudeRulePath, claudeRule);
+            console.error('CodeAtlas: Generated CLAUDE.md');
+        }
+        catch {
+            // Skip silently
+        }
+    }
+    // === Windsurf: .windsurfrules ===
+    const windsurfRulePath = path.join(workspaceRoot, '.windsurfrules');
+    if (!fs.existsSync(windsurfRulePath)) {
+        try {
+            fs.writeFileSync(windsurfRulePath, codeatlasRule);
+            console.error('CodeAtlas: Generated .windsurfrules');
+        }
+        catch {
+            // Skip silently
+        }
+    }
+}
+//# sourceMappingURL=memoryGenerator.js.map

package/dist/src/memoryGenerator.js.map

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package/dist/src/oracleDatabase.js

@@ -0,0 +1,298 @@
+import oracledb from "oracledb";
+import { authStorage } from "./context.js";
+// Connection configuration derived from environment variables
+const dbConfig = {
+    user: process.env.ORACLE_USER || "ADMIN",
+    password: process.env.ORACLE_PASSWORD || "",
+    connectString: process.env.ORACLE_CONN_STRING || ""
+};
+/**
+ * Service to manage AI Memory on Oracle Database 26ai.
+ * Employs Thick Mode (via Oracle Instant Client) to support stable mTLS connections.
+ */
+export class OracleMemoryService {
+    static pool = null;
+    /**
+     * Initializes the Connection Pool
+     */
+    static async init() {
+        if (!this.pool) {
+            try {
+                // Activate Thick Mode by pointing to the Oracle Instant Client directory
+                if (process.env.ORACLE_LIB_DIR) {
+                    console.log("🚀 Initializing Oracle Client in Thick Mode...");
+                    oracledb.initOracleClient({
+                        libDir: process.env.ORACLE_LIB_DIR,
+                        configDir: process.env.ORACLE_WALLET_DIR // Contains tnsnames.ora and wallet files
+                    });
+                }
+                // Configure standard data formats for Oracle 26ai
+                oracledb.outFormat = oracledb.OUT_FORMAT_OBJECT;
+                oracledb.fetchAsString = [oracledb.CLOB];
+                this.pool = await oracledb.createPool({
+                    ...dbConfig,
+                    poolMin: 2,
+                    poolMax: 10,
+                    poolIncrement: 1
+                });
+                console.log("✅ Oracle 26ai DB Pool initialized successfully (Thick Mode)");
+            }
+            catch (err) {
+                console.error("❌ Failed to initialize Oracle DB pool:", err instanceof Error ? err.message : String(err));
+                throw err;
+            }
+        }
+        return this.pool;
+    }
+    /**
+     * Configures the Session Context for Row-Level Security (Oracle Virtual Private Database)
+     */
+    static async setSessionContext(connection) {
+        const auth = authStorage.getStore();
+        const tenantId = auth ? auth.uid : "admin";
+        try {
+            // Invoke the context package to dynamically apply Row-Level Security row-filtering policies
+            const sql = `BEGIN ADMIN.codeatlas_ctx_pkg.set_tenant(:tenantId); END;`;
+            await connection.execute(sql, { tenantId });
+            console.log(`[Oracle RLS] Security Context set for tenant: ${tenantId}`);
+        }
+        catch (err) {
+            console.error("[Oracle RLS] Failed to set security context:", err instanceof Error ? err.message : String(err));
+            // Do not block execution if package/context is not installed (prevents local dev crashes)
+            if (process.env.NODE_ENV === "production") {
+                throw err;
+            }
+        }
+    }
+    /**
+     * Tier 1: Episodic JSON - Stores business events (Business Rules / Change Logs)
+     */
+    static async saveEpisodicMemory(project, eventType, data) {
+        let connection;
+        try {
+            const pool = await this.init();
+            connection = await pool.getConnection();
+            await this.setSessionContext(connection);
+            const id = `${project}_${eventType}_${Date.now()}`;
+            const auth = authStorage.getStore();
+            const tenantId = auth ? auth.uid : "admin";
+            const sql = `
+          INSERT INTO ai_episodic_memory (id, project_name, event_type, event_data, tenant_id)
+          VALUES (:id, :project, :eventType, :data, :tenantId)
+        `;
+            await connection.execute(sql, {
+                id,
+                project,
+                eventType,
+                data: { val: data, type: oracledb.DB_TYPE_JSON },
+                tenantId
+            }, { autoCommit: true });
+        }
+        catch (err) {
+            console.error("Error saving episodic memory:", err instanceof Error ? err.message : String(err));
+        }
+        finally {
+            if (connection) {
+                try {
+                    await connection.close();
+                }
+                catch (closeErr) {
+                    console.error("Error closing connection:", closeErr);
+                }
+            }
+        }
+    }
+    /**
+     * Tier 2: Semantic Memory - Stores code entity embeddings
+     */
+    static async saveSemanticMemory(project, entities) {
+        let connection;
+        try {
+            const pool = await this.init();
+            connection = await pool.getConnection();
+            await this.setSessionContext(connection);
+            const auth = authStorage.getStore();
+            const tenantId = auth ? auth.uid : "admin";
+            const sql = `
+          MERGE INTO ai_semantic_memory trg
+          USING (SELECT :id AS id, :project AS project_name, :type AS entity_type, :name AS entity_name, :path AS file_path, :content AS content, :tenantId AS tenant_id FROM DUAL) src
+          ON (trg.id = src.id)
+          WHEN MATCHED THEN UPDATE SET trg.content = src.content
+          WHEN NOT MATCHED THEN INSERT (id, project_name, entity_type, entity_name, file_path, content, tenant_id)
+          VALUES (src.id, src.project_name, src.entity_type, src.entity_name, src.file_path, src.content, src.tenant_id)
+        `;
+            const binds = entities.map(e => ({
+                id: `${project}_${e.id}`,
+                project,
+                type: e.type,
+                name: e.label,
+                path: e.filePath || "",
+                content: `Entity: ${e.label}, Type: ${e.type}, Path: ${e.filePath}`,
+                tenantId
+            }));
+            await connection.executeMany(sql, binds, { autoCommit: true });
+        }
+        catch (err) {
+            console.error("Error saving semantic memory:", err instanceof Error ? err.message : String(err));
+        }
+        finally {
+            if (connection) {
+                try {
+                    await connection.close();
+                }
+                catch (closeErr) {
+                    console.error("Error closing connection:", closeErr);
+                }
+            }
+        }
+    }
+    /**
+     * Tier 3: Relational Memory - Stores relationships (Knowledge Graph)
+     */
+    static async saveRelationalMemory(project, links) {
+        let connection;
+        try {
+            const pool = await this.init();
+            connection = await pool.getConnection();
+            await this.setSessionContext(connection);
+            const auth = authStorage.getStore();
+            const tenantId = auth ? auth.uid : "admin";
+            const sql = `
+          MERGE INTO ai_relational_memory trg
+          USING (SELECT :src AS source_id, :tgt AS target_id, :project AS project_name, :type AS relationship_type, :tenantId AS tenant_id FROM DUAL) src
+          ON (trg.source_id = src.source_id AND trg.target_id = src.target_id AND trg.relationship_type = src.relationship_type AND trg.tenant_id = src.tenant_id)
+          WHEN NOT MATCHED THEN INSERT (source_id, target_id, project_name, relationship_type, tenant_id)
+          VALUES (src.source_id, src.target_id, src.project_name, src.relationship_type, src.tenant_id)
+        `;
+            const binds = links.map(l => ({
+                src: `${project}_${l.source}`,
+                tgt: `${project}_${l.target}`,
+                project,
+                type: l.type,
+                tenantId
+            }));
+            await connection.executeMany(sql, binds, { autoCommit: true });
+        }
+        catch (err) {
+            console.error("Error saving relational memory:", err instanceof Error ? err.message : String(err));
+        }
+        finally {
+            if (connection) {
+                try {
+                    await connection.close();
+                }
+                catch (closeErr) {
+                    console.error("Error closing connection:", closeErr);
+                }
+            }
+        }
+    }
+    /**
+     * Query using AI Vector Search (Native Oracle 26ai feature)
+     */
+    static async searchSemanticMemory(project, query, limit = 5) {
+        let connection;
+        try {
+            const pool = await this.init();
+            connection = await pool.getConnection();
+            await this.setSessionContext(connection);
+            const sql = `
+          SELECT entity_name, entity_type, file_path, content
+          FROM ai_semantic_memory
+          WHERE project_name = :project
+          ORDER BY VECTOR_DISTANCE(embedding, VECTOR_EMBEDDING(my_model USING :query), COSINE)
+          FETCH FIRST :limit ROWS ONLY
+        `;
+            const result = await connection.execute(sql, { project, query, limit });
+            return result.rows;
+        }
+        catch (err) {
+            console.error("Error searching semantic memory:", err instanceof Error ? err.message : String(err));
+            return [];
+        }
+        finally {
+            if (connection) {
+                try {
+                    await connection.close();
+                }
+                catch (closeErr) {
+                    console.error("Error closing connection:", closeErr);
+                }
+            }
+        }
+    }
+    /**
+     * Graph Analysis: Detect architectural smells (Circular Dependencies, God Objects, Dead Code)
+     * Utilizing SQL Property Graph Queries (Oracle 23ai+)
+     */
+    static async detectArchitecturalSmells(project) {
+        let connection;
+        try {
+            const pool = await this.init();
+            connection = await pool.getConnection();
+            await this.setSessionContext(connection);
+            const smells = {
+                circularDependencies: [],
+                godObjects: [],
+                deadCode: []
+            };
+            // 1. Detect Circular Dependencies (Cycles in the dependency graph) using SQL Graph queries
+            const circularSql = `
+          SELECT DISTINCT entity_name, file_path
+          FROM GRAPH_TABLE ( ai_knowledge_graph
+            MATCH (a)-[e IS ai_relational_memory]->{1,5}(a)
+            WHERE a.project_name = :project
+            COLUMNS (a.entity_name, a.file_path)
+          )
+        `;
+            const circularRes = await connection.execute(circularSql, { project });
+            smells.circularDependencies = circularRes.rows;
+            // 2. Detect God Objects (Entities with excessively high incoming relationships / high in-degree)
+            const godSql = `
+          SELECT entity_name, entity_type, file_path, in_degree
+          FROM (
+            SELECT target_id, count(*) as in_degree
+            FROM ai_relational_memory
+            WHERE project_name = :project
+            GROUP BY target_id
+          ) r
+          JOIN ai_semantic_memory s ON r.target_id = s.id
+          WHERE in_degree > 15
+          ORDER BY in_degree DESC
+          FETCH FIRST 10 ROWS ONLY
+        `;
+            const godRes = await connection.execute(godSql, { project });
+            smells.godObjects = godRes.rows;
+            // 3. Detect Dead Code (Entities with zero incoming relationships, and not main entry points)
+            const deadSql = `
+          SELECT entity_name, file_path
+          FROM ai_semantic_memory s
+          WHERE project_name = :project
+            AND entity_type IN ('function', 'class')
+            AND NOT EXISTS (
+              SELECT 1 FROM ai_relational_memory r 
+              WHERE r.target_id = s.id
+            )
+          FETCH FIRST 20 ROWS ONLY
+        `;
+            const deadRes = await connection.execute(deadSql, { project });
+            smells.deadCode = deadRes.rows;
+            return smells;
+        }
+        catch (err) {
+            console.error("Error detecting smells:", err instanceof Error ? err.message : String(err));
+            return null;
+        }
+        finally {
+            if (connection) {
+                try {
+                    await connection.close();
+                }
+                catch (closeErr) {
+                    console.error("Error closing connection:", closeErr);
+                }
+            }
+        }
+    }
+}
+//# sourceMappingURL=oracleDatabase.js.map

package/dist/src/oracleDatabase.js.map

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