agentopology 0.1.1 → 0.2.0

package/README.md

@@ -352,7 +352,7 @@ mcp-servers {
 </tr>
 </table>
 
-Plus: schemas, artifacts, metering, circuit breakers, scale configs, depth levels, environment overrides, prompt variants, composition via imports, and [more](spec/grammar.md).
+Plus: **memory stores** (semantic, graph, episodic — 11 backends), **retrieval strategies** (scoring weights, cache-hit routing), schemas, artifacts, metering, circuit breakers, scale configs, depth levels, environment overrides, prompt variants, composition via imports, and [more](spec/grammar.md).
 
 ---
 

package/dist/analyzer/index.d.ts

@@ -15,6 +15,7 @@ export interface TopologySummary {
         groups: number;
         humans: number;
         orchestrators: number;
+        stores: number;
     };
     edgeCount: number;
     declaredPatterns: string[];

package/dist/analyzer/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/analyzer/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EACV,WAAW,EAOZ,MAAM,kBAAkB,CAAC;AAM1B,MAAM,WAAW,eAAe;IAC9B,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;IAChB,WAAW,EAAE,MAAM,CAAC;IACpB,SAAS,EAAE;QACT,MAAM,EAAE,MAAM,CAAC;QACf,OAAO,EAAE,MAAM,CAAC;QAChB,KAAK,EAAE,MAAM,CAAC;QACd,MAAM,EAAE,MAAM,CAAC;QACf,MAAM,EAAE,MAAM,CAAC;QACf,aAAa,EAAE,MAAM,CAAC;KACvB,CAAC;IACF,SAAS,EAAE,MAAM,CAAC;IAClB,gBAAgB,EAAE,MAAM,EAAE,CAAC;CAC5B;AAED,MAAM,WAAW,eAAe;IAC9B,IAAI,EAAE,MAAM,CAAC;IACb,UAAU,EAAE,UAAU,GAAG,QAAQ,CAAC;IAClC,aAAa,EAAE,MAAM,EAAE,CAAC;IACxB,WAAW,EAAE,MAAM,CAAC;CACrB;AAED,MAAM,WAAW,SAAS;IACxB,KAAK,EAAE,MAAM,CAAC;IACd,KAAK,EAAE,MAAM,EAAE,CAAC;CACjB;AAED,MAAM,WAAW,UAAU;IACzB,KAAK,EAAE,MAAM,GAAG,aAAa,CAAC;IAC9B,OAAO,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAED,MAAM,WAAW,cAAc;IAC7B,OAAO,EAAE,eAAe,CAAC;IACzB,QAAQ,EAAE,eAAe,EAAE,CAAC;IAC5B,MAAM,EAAE,SAAS,EAAE,CAAC;IACpB,WAAW,EAAE,UAAU,EAAE,CAAC;CAC3B;AA2SD,wBAAgB,OAAO,CAAC,GAAG,EAAE,WAAW,GAAG,cAAc,CAsCxD"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/analyzer/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EACV,WAAW,EAOZ,MAAM,kBAAkB,CAAC;AAM1B,MAAM,WAAW,eAAe;IAC9B,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;IAChB,WAAW,EAAE,MAAM,CAAC;IACpB,SAAS,EAAE;QACT,MAAM,EAAE,MAAM,CAAC;QACf,OAAO,EAAE,MAAM,CAAC;QAChB,KAAK,EAAE,MAAM,CAAC;QACd,MAAM,EAAE,MAAM,CAAC;QACf,MAAM,EAAE,MAAM,CAAC;QACf,aAAa,EAAE,MAAM,CAAC;QACtB,MAAM,EAAE,MAAM,CAAC;KAChB,CAAC;IACF,SAAS,EAAE,MAAM,CAAC;IAClB,gBAAgB,EAAE,MAAM,EAAE,CAAC;CAC5B;AAED,MAAM,WAAW,eAAe;IAC9B,IAAI,EAAE,MAAM,CAAC;IACb,UAAU,EAAE,UAAU,GAAG,QAAQ,CAAC;IAClC,aAAa,EAAE,MAAM,EAAE,CAAC;IACxB,WAAW,EAAE,MAAM,CAAC;CACrB;AAED,MAAM,WAAW,SAAS;IACxB,KAAK,EAAE,MAAM,CAAC;IACd,KAAK,EAAE,MAAM,EAAE,CAAC;CACjB;AAED,MAAM,WAAW,UAAU;IACzB,KAAK,EAAE,MAAM,GAAG,aAAa,CAAC;IAC9B,OAAO,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAED,MAAM,WAAW,cAAc;IAC7B,OAAO,EAAE,eAAe,CAAC;IACzB,QAAQ,EAAE,eAAe,EAAE,CAAC;IAC5B,MAAM,EAAE,SAAS,EAAE,CAAC;IACpB,WAAW,EAAE,UAAU,EAAE,CAAC;CAC3B;AAsVD,wBAAgB,OAAO,CAAC,GAAG,EAAE,WAAW,GAAG,cAAc,CAuCxD"}

package/dist/analyzer/index.js

@@ -199,6 +199,16 @@ function detectPatterns(ast) {
             description: `Group: ${group.id} (${(group.members ?? []).join(", ")})`,
         });
     }
+    // Memory infrastructure: detect if stores are present
+    if (ast.stores && ast.stores.length > 0) {
+        const storeIds = ast.stores.map((s) => s.id);
+        patterns.push({
+            name: "memory-infrastructure",
+            confidence: "definite",
+            involvedNodes: storeIds,
+            description: `Memory stores: ${storeIds.join(", ")}`,
+        });
+    }
     return patterns;
 }
 // ---------------------------------------------------------------------------
@@ -242,6 +252,30 @@ function generateSuggestions(ast) {
             });
         }
     }
+    // Memory-related suggestions
+    const hasStores = ast.stores && ast.stores.length > 0;
+    const hasRetrievals = ast.retrievals && ast.retrievals.length > 0;
+    if (hasStores) {
+        // Check if agents have memory stores assigned
+        const agentsWithMemory = ast.nodes.filter((n) => isAgent(n) && (n.memory != null && n.memory.length > 0));
+        const agentsWithoutMemory = ast.nodes.filter((n) => isAgent(n) && (!n.memory || n.memory.length === 0));
+        if (agentsWithoutMemory.length > 0 && agentsWithMemory.length > 0) {
+            for (const agent of agentsWithoutMemory) {
+                suggestions.push({
+                    level: "info",
+                    message: "Agent has no memory stores assigned — consider assigning memory stores to this agent",
+                    node: agent.id,
+                });
+            }
+        }
+        // Check if stores exist but no retrieval strategy
+        if (!hasRetrievals) {
+            suggestions.push({
+                level: "improvement",
+                message: "Memory stores exist but no retrieval strategy is defined — consider adding a retrieval strategy",
+            });
+        }
+    }
     // Declared vs detected pattern mismatch
     const detected = detectPatterns(ast);
     const detectedNames = new Set(detected.map((p) => p.name));
@@ -268,6 +302,7 @@ export function analyze(ast) {
         groups: 0,
         humans: 0,
         orchestrators: 0,
+        stores: ast.stores ? ast.stores.length : 0,
     };
     for (const node of ast.nodes) {
         switch (node.type) {

package/dist/analyzer/index.js.map

@@ -1 +1 @@
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package/dist/bindings/claude-code.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"claude-code.d.ts","sourceRoot":"","sources":["../../src/bindings/claude-code.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAsBH,OAAO,KAAK,EAAE,aAAa,EAAiB,MAAM,YAAY,CAAC;AAohE/D,kEAAkE;AAClE,eAAO,MAAM,iBAAiB,EAAE,aAuF/B,CAAC"}
+{"version":3,"file":"claude-code.d.ts","sourceRoot":"","sources":["../../src/bindings/claude-code.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAuBH,OAAO,KAAK,EAAE,aAAa,EAAiB,MAAM,YAAY,CAAC;AA+yE/D,kEAAkE;AAClE,eAAO,MAAM,iBAAiB,EAAE,aA0F/B,CAAC"}

package/dist/bindings/claude-code.js

@@ -352,6 +352,103 @@ function generateAgents(ast) {
             }
             sections.push("");
         }
+        // Memory stores — rich instructions with store details and access methods
+        if (agent.memory && agent.memory.length > 0) {
+            const storeMap = new Map((ast.stores ?? []).map(s => [s.id, s]));
+            sections.push("## Memory Stores");
+            sections.push("");
+            sections.push("You have access to the following memory stores. Use them to persist and retrieve knowledge across conversations.");
+            sections.push("");
+            for (const storeId of agent.memory) {
+                const store = storeMap.get(storeId);
+                if (!store) {
+                    sections.push(`### ${storeId}`);
+                    sections.push(`- Store not found in topology`);
+                    sections.push("");
+                    continue;
+                }
+                sections.push(`### ${storeId}`);
+                if (store.description)
+                    sections.push(store.description);
+                sections.push("");
+                sections.push(`- **Type**: ${store.type}`);
+                sections.push(`- **Backend**: ${store.backend}`);
+                if (store.path)
+                    sections.push(`- **Path**: \`${store.path}\``);
+                if (store.scope)
+                    sections.push(`- **Scope**: ${store.scope}`);
+                // Access method — MCP or skill-based
+                const hasMcp = STORE_MCP_COMMANDS[store.backend] != null;
+                if (hasMcp) {
+                    sections.push(`- **Access**: MCP server \`${storeId}\` (auto-configured in .mcp.json)`);
+                }
+                else if (store.path) {
+                    sections.push(`- **Access**: Direct file access at \`${store.path}\``);
+                }
+                // Embedding config
+                if (store.embedding) {
+                    sections.push(`- **Embedding**: ${store.embedding.model} (${store.embedding.provider}, ${store.embedding.dimensions}d)`);
+                }
+                // Search strategy
+                if (store.search) {
+                    const parts = [`strategy: ${store.search.strategy}`];
+                    if (store.search.topK)
+                        parts.push(`top-k: ${store.search.topK}`);
+                    if (store.search.rerank)
+                        parts.push(`rerank: yes`);
+                    sections.push(`- **Search**: ${parts.join(", ")}`);
+                }
+                // Ingestion sources
+                if (store.ingestion?.sources) {
+                    sections.push(`- **Ingestion sources**: ${store.ingestion.sources.join(", ")}`);
+                }
+                // Lifecycle
+                if (store.lifecycle?.retention) {
+                    sections.push(`- **Retention**: ${store.lifecycle.retention}`);
+                }
+                sections.push("");
+            }
+        }
+        // Retrieval strategy — rich details
+        if (agent.retrieval) {
+            const retrieval = (ast.retrievals ?? []).find(r => r.id === agent.retrieval);
+            if (retrieval) {
+                sections.push("## Retrieval Strategy");
+                sections.push("");
+                sections.push(`**${retrieval.id}** — When you need to recall information, use this strategy:`);
+                sections.push("");
+                if (retrieval.sources)
+                    sections.push(`- **Sources**: ${retrieval.sources.join(", ")}`);
+                if (retrieval.budget)
+                    sections.push(`- **Token budget**: ${retrieval.budget} tokens max for retrieved context`);
+                if (retrieval.paths)
+                    sections.push(`- **Search paths**: ${retrieval.paths.join(", ")}`);
+                if (retrieval.rerank)
+                    sections.push(`- **Reranking**: enabled — results are cross-ranked for relevance`);
+                if (retrieval.diversity)
+                    sections.push(`- **Diversity**: enabled — results span different sources`);
+                if (retrieval.cacheHitThreshold != null) {
+                    sections.push(`- **Cache hit**: threshold ${retrieval.cacheHitThreshold} → ${retrieval.cacheHitAction ?? "short-circuit"}`);
+                }
+                if (retrieval.scoring) {
+                    const s = retrieval.scoring;
+                    const weights = [];
+                    if (s.recencyWeight != null)
+                        weights.push(`recency: ${s.recencyWeight}`);
+                    if (s.semanticWeight != null)
+                        weights.push(`semantic: ${s.semanticWeight}`);
+                    if (s.importanceWeight != null)
+                        weights.push(`importance: ${s.importanceWeight}`);
+                    if (weights.length)
+                        sections.push(`- **Scoring weights**: ${weights.join(", ")}`);
+                }
+                sections.push("");
+            }
+            else {
+                sections.push(`Retrieval strategy: ${agent.retrieval}`);
+                sections.push("");
+            }
+        }
         // Outputs section
         if (agent.outputs) {
             sections.push("## Outputs");
@@ -1085,6 +1182,30 @@ function generateTopologySkill(ast) {
             sections.push("");
         }
     }
+    // Memory Stores
+    const stores = ast.stores ?? [];
+    if (stores.length > 0) {
+        sections.push("## Memory Stores");
+        sections.push("");
+        for (const store of stores) {
+            sections.push(`### ${store.id}`);
+            sections.push(`- Type: ${store.type}`);
+            sections.push(`- Backend: ${store.backend}`);
+            if (store.path)
+                sections.push(`- Path: ${store.path}`);
+            if (store.connection)
+                sections.push(`- Connection: ${store.connection}`);
+            if (store.scope)
+                sections.push(`- Scope: ${store.scope}`);
+            if (store.search?.strategy)
+                sections.push(`- Search: ${store.search.strategy}`);
+            if (store.embedding?.model)
+                sections.push(`- Embedding: ${store.embedding.model}`);
+            if (store.lifecycle?.retention)
+                sections.push(`- Retention: ${store.lifecycle.retention}`);
+            sections.push("");
+        }
+    }
     files.push({
         path: `.claude/skills/${name}/SKILL.md`,
         content: sections.join("\n") + "\n",
@@ -1188,6 +1309,109 @@ function generateMemory(ast) {
     if (memory.workspace) {
         files.push(gitkeep(`.claude/skills/${name}/runs`));
     }
+    // Store directory markers
+    const stores = ast.stores ?? [];
+    for (const store of stores) {
+        files.push(gitkeep(`.claude/stores/${store.id}`));
+    }
+    return files;
+}
+/**
+ * Generate memory command files for each store.
+ *
+ * These are Claude Code slash-commands (`.claude/commands/`) that give agents
+ * a concrete way to interact with memory stores — search, ingest, and inspect.
+ * This works alongside (or instead of) MCP servers.
+ */
+function generateMemoryCommands(ast) {
+    const files = [];
+    const stores = ast.stores ?? [];
+    for (const store of stores) {
+        // Search command — for stores with search config or semantic/episodic type
+        if (store.search || store.type === "semantic" || store.type === "episodic") {
+            const hasMcp = STORE_MCP_COMMANDS[store.backend] != null;
+            const searchLines = [
+                "---",
+                `description: "Search the ${store.id} memory store"`,
+                "---",
+                "",
+                `# /memory-search-${store.id}`,
+                "",
+                `Search the **${store.id}** store for relevant information.`,
+                "",
+                `## Store Details`,
+                `- **Type**: ${store.type}`,
+                `- **Backend**: ${store.backend}`,
+            ];
+            if (store.path)
+                searchLines.push(`- **Path**: \`${store.path}\``);
+            if (store.search) {
+                searchLines.push(`- **Strategy**: ${store.search.strategy}`);
+                if (store.search.topK)
+                    searchLines.push(`- **Top-K**: ${store.search.topK}`);
+                if (store.search.rerank)
+                    searchLines.push(`- **Reranking**: enabled`);
+            }
+            if (store.embedding) {
+                searchLines.push(`- **Embedding**: ${store.embedding.model} (${store.embedding.provider}, ${store.embedding.dimensions}d)`);
+            }
+            searchLines.push("");
+            searchLines.push("## Instructions");
+            searchLines.push("");
+            if (hasMcp) {
+                searchLines.push(`Use the \`${store.id}\` MCP server to search this store.`);
+                searchLines.push(`The MCP server is configured in \`.mcp.json\` and provides tools for querying the ${store.backend} database.`);
+            }
+            else {
+                searchLines.push(`This store uses ${store.backend} at \`${store.path ?? ".claude/stores/" + store.id}\`.`);
+                searchLines.push(`Read the database directly or use an appropriate library to query it.`);
+            }
+            searchLines.push("");
+            searchLines.push("Search for: $ARGUMENTS");
+            searchLines.push("");
+            files.push({
+                path: `.claude/commands/memory-search-${store.id}.md`,
+                content: searchLines.join("\n"),
+                category: "machine",
+            });
+        }
+        // Ingest command — for stores with ingestion config
+        if (store.ingestion) {
+            const ingestLines = [
+                "---",
+                `description: "Ingest documents into the ${store.id} memory store"`,
+                "---",
+                "",
+                `# /memory-ingest-${store.id}`,
+                "",
+                `Ingest documents into the **${store.id}** store.`,
+                "",
+                "## Ingestion Config",
+                `- **Sources**: ${store.ingestion.sources?.join(", ") ?? "not specified"}`,
+                `- **Chunking**: ${store.ingestion.chunking ?? "recursive"}`,
+            ];
+            if (store.ingestion.chunkSize)
+                ingestLines.push(`- **Chunk size**: ${store.ingestion.chunkSize}`);
+            if (store.ingestion.overlap)
+                ingestLines.push(`- **Overlap**: ${store.ingestion.overlap}`);
+            if (store.embedding) {
+                ingestLines.push(`- **Embedding**: ${store.embedding.model} (${store.embedding.provider}, ${store.embedding.dimensions}d)`);
+            }
+            ingestLines.push("");
+            ingestLines.push("## Instructions");
+            ingestLines.push("");
+            ingestLines.push(`1. Read files from the configured sources: ${store.ingestion.sources?.join(", ") ?? "docs/"}`);
+            ingestLines.push(`2. Split content into chunks (${store.ingestion.chunking ?? "recursive"}, size: ${store.ingestion.chunkSize ?? 512})`);
+            ingestLines.push(`3. Generate embeddings using ${store.embedding?.model ?? "the configured model"}`);
+            ingestLines.push(`4. Insert into ${store.backend} at \`${store.path ?? ".claude/stores/" + store.id}\``);
+            ingestLines.push("");
+            files.push({
+                path: `.claude/commands/memory-ingest-${store.id}.md`,
+                content: ingestLines.join("\n"),
+                category: "machine",
+            });
+        }
+    }
     return files;
 }
 /** Generate gate script stubs. */
@@ -1483,9 +1707,34 @@ function generateSettings(ast) {
         category: "shared-config",
     };
 }
-/** Generate .mcp.json from mcp-servers block. Always includes env field. */
+/**
+ * Backend → MCP server mapping.
+ *
+ * Only packages verified to exist on npm or PyPI are included.
+ * npm packages use `npx -y`, Python packages use `uvx`.
+ * `pathFlag` controls how the DB path is passed (positional, --db, --db-path, etc.).
+ *
+ * Verified 2026-03-21:
+ *   npm:  kuzu-mcp-server@0.1.0, mongodb-mcp-server@1.8.1
+ *   pip:  mcp-server-sqlite@2025.4.25, mcp-server-qdrant@0.8.1,
+ *         mcp-server-neo4j@0.1.8, chroma-mcp@0.2.6
+ */
+const STORE_MCP_COMMANDS = {
+    // npm packages
+    "kuzu": { command: "npx", args: ["-y", "kuzu-mcp-server"] }, // positional
+    "mongodb": { command: "npx", args: ["-y", "mongodb-mcp-server"], pathFlag: "--uri" },
+    // Python MCP servers (via uvx)
+    "sqlite": { command: "uvx", args: ["mcp-server-sqlite"], pathFlag: "--db-path" },
+    "sqlite-vec": { command: "uvx", args: ["mcp-server-sqlite"], pathFlag: "--db-path" },
+    "qdrant": { command: "uvx", args: ["mcp-server-qdrant"], pathFlag: "--qdrant-url" },
+    "neo4j": { command: "uvx", args: ["mcp-server-neo4j"], pathFlag: "--db-uri" },
+    "chroma": { command: "uvx", args: ["chroma-mcp"], pathFlag: "--host" },
+    // No verified MCP servers: lancedb, pinecone, pgvector, falkordb
+    // These backends use skill-based access (slash commands) instead
+};
 function generateMcpJson(ast) {
-    if (Object.keys(ast.mcpServers).length === 0)
+    const stores = ast.stores ?? [];
+    if (Object.keys(ast.mcpServers).length === 0 && stores.length === 0)
         return null;
     const mcpConfig = { mcpServers: {} };
     const servers = mcpConfig.mcpServers;
@@ -1512,6 +1761,36 @@ function generateMcpJson(ast) {
         }
         servers[name] = entry;
     }
+    // Merge memory store MCP server entries
+    for (const store of stores) {
+        const mcpCmd = STORE_MCP_COMMANDS[store.backend];
+        if (!mcpCmd) {
+            // Backend not in the known MCP map — skip (skill-based access only)
+            continue;
+        }
+        const args = [...mcpCmd.args];
+        const storePath = store.path ?? `.claude/stores/${store.id}`;
+        // Each server has its own CLI convention for the DB path
+        if (mcpCmd.pathFlag) {
+            args.push(mcpCmd.pathFlag, storePath);
+        }
+        else {
+            // No pathFlag = positional argument (e.g., kuzu-mcp-server ./path)
+            args.push(storePath);
+        }
+        const env = {};
+        if (store.connection) {
+            env.CONNECTION_STRING = store.connection;
+        }
+        servers[store.id] = {
+            command: mcpCmd.command,
+            args,
+            env,
+        };
+    }
+    // If no servers were added (all stores had unsupported backends), return null
+    if (Object.keys(servers).length === 0)
+        return null;
     return {
         path: ".mcp.json",
         content: JSON.stringify(mcpConfig, null, 2) + "\n",
@@ -2026,6 +2305,8 @@ export const claudeCodeBinding = {
         files.push(...generateSchemas(ast));
         // Memory directories
         files.push(...generateMemory(ast));
+        // Memory store command files (search/ingest per store)
+        files.push(...generateMemoryCommands(ast));
         // Gate scripts
         files.push(...generateGateScripts(ast));
         files.push(...generateGateWrapperScripts(ast));