vexp-cli 1.2.14 → 1.2.16

package/dist/agent-config.js

@@ -16,6 +16,7 @@ const VEXP_MARKER_RE = /<!-- vexp(?:\s+v[\d.]+)? -->/;
 const VEXP_MARKER_END = "<!-- /vexp -->";
 // All vexp MCP tools (all read-only — safe to pre-approve).
 const VEXP_TOOLS = [
+    "run_pipeline",
     "get_context_capsule",
     "get_impact_graph",
     "search_logic_flow",
@@ -149,8 +150,8 @@ export function configureAgents(workspaceRoot, binaryPath, version, agentFilter)
                     customCommands: [
                         {
                             name: "vexp-context",
-                            description: "Get vexp context capsule for current task",
-                            prompt: "{{{ input }}}\n\nFirst, call get_context_capsule with the above task description.",
+                            description: "Get vexp context for current task",
+                            prompt: "{{{ input }}}\n\nFirst, call run_pipeline with the above task description.",
                         },
                     ],
                     contextProviders: [
@@ -229,12 +230,19 @@ function appendOrCreate(filePath, content, version) {
         fs.appendFileSync(filePath, "\n\n" + content);
         return "appended";
     }
-    const versionMatch = markerMatch[0].match(/v([\d.]+)/);
-    if (versionMatch && versionMatch[1] === version)
-        return "skipped";
-    const startIdx = existing.indexOf(markerMatch[0]);
+    // Find start of the LINE containing the marker (not the marker itself).
+    // The marker may be mid-line (e.g. `## heading <!-- vexp v1.2.14 -->`),
+    // so we walk backwards to the previous newline to avoid duplicating the heading.
+    const markerIdx = existing.indexOf(markerMatch[0]);
+    let startIdx = markerIdx;
+    while (startIdx > 0 && existing[startIdx - 1] !== '\n') {
+        startIdx--;
+    }
     const endIdx = existing.indexOf(VEXP_MARKER_END);
     if (endIdx !== -1) {
+        const existingSection = existing.substring(startIdx, endIdx + VEXP_MARKER_END.length);
+        if (existingSection === content)
+            return "skipped"; // truly identical → no write
         const before = existing.substring(0, startIdx);
         const after = existing.substring(endIdx + VEXP_MARKER_END.length);
         fs.writeFileSync(filePath, before + content + after, "utf-8");
@@ -255,27 +263,31 @@ function mergeJsonConfig(filePath, mergePayload, version) {
             // Malformed JSON: overwrite
         }
     }
-    const existingVersion = existing.__vexp_version ?? (existing.__vexp ? "0.0.0" : undefined);
-    if (existingVersion === version)
-        return "skipped";
+    // Build the merged result first, then compare to avoid unnecessary writes.
+    const merged = { ...existing };
     for (const [key, value] of Object.entries(mergePayload)) {
         if (typeof value === "object" && value !== null && !Array.isArray(value)) {
-            existing[key] = {
-                ...(existing[key] ?? {}),
+            merged[key] = {
+                ...(merged[key] ?? {}),
                 ...value,
             };
         }
-        else if (Array.isArray(value) && Array.isArray(existing[key])) {
-            existing[key] = [...existing[key], ...value];
+        else if (Array.isArray(value) && Array.isArray(merged[key])) {
+            merged[key] = [...merged[key], ...value];
         }
         else {
-            existing[key] = value;
+            merged[key] = value;
         }
     }
-    delete existing.__vexp;
-    existing.__vexp_version = version;
+    delete merged.__vexp;
+    merged.__vexp_version = version;
+    // Compare serialized output — skip if truly identical
+    const mergedStr = JSON.stringify(merged, null, 2);
+    const existingStr = JSON.stringify(existing, null, 2);
+    if (mergedStr === existingStr)
+        return "skipped";
     fs.mkdirSync(path.dirname(filePath), { recursive: true });
-    fs.writeFileSync(filePath, JSON.stringify(existing, null, 2), "utf-8");
+    fs.writeFileSync(filePath, mergedStr, "utf-8");
     return "merged";
 }
 // ---------------------------------------------------------------------------
@@ -433,95 +445,90 @@ function generateAgentConfig(template, vars) {
 function claudeCodeTemplate(vars) {
     return `## vexp — Context-Aware AI Coding <!-- vexp v${vars.version} -->
 
-### MANDATORY: use vexp MCP tools before ANYTHING else
-For every task — questions, bug fixes, features, exploration:
-**call the \`get_context_capsule\` MCP tool first**.
-
-Do NOT use grep, glob, Bash, or Read to search/explore the codebase.
-Use vexp MCP tools instead — they return pre-indexed, relevant context.
-
-### Available MCP tools (invoke via tool interface, NOT via HTTP or bash)
-- \`get_context_capsule\` — most relevant code for your task or question (ALWAYS FIRST)
-- \`get_impact_graph\` — what breaks if you change a symbol
-- \`search_logic_flow\` — execution paths between functions
-- \`get_skeleton\` — token-efficient file structure
+### MANDATORY: use vexp pipeline — do NOT grep, glob, or Read files
+For every task — bug fixes, features, refactors, debugging:
+**call \`run_pipeline\` FIRST**. It executes context search + impact analysis +
+memory recall in a single call, returning compressed results.
+
+Do NOT use grep, glob, Bash, Read, or cat to search/explore the codebase.
+vexp returns pre-indexed, graph-ranked context that is more relevant and
+uses fewer tokens than manual file reading.
+
+### Primary Tool
+- \`run_pipeline\` — **USE THIS FOR EVERYTHING**. Single call that runs
+  capsule + impact + memory server-side. Returns compressed results.
+  Auto-detects intent (debug/modify/refactor/explore) from your task.
+  Includes full file content for pivots (no need to Read files).
+  Examples:
+  - \`run_pipeline({ "task": "fix JWT validation bug" })\` — auto-detect
+  - \`run_pipeline({ "task": "refactor db layer", "preset": "refactor" })\` — explicit
+  - \`run_pipeline({ "task": "add auth", "observation": "using JWT" })\` — save insight in same call
+
+### Other MCP tools (use only when run_pipeline is insufficient)
+- \`get_context_capsule\` — lightweight alternative for simple questions only
+- \`get_impact_graph\` — standalone deep impact analysis of a specific symbol
+- \`search_logic_flow\` — trace execution paths between two specific symbols
+- \`get_skeleton\` — token-efficient file structure for a specific file
 - \`index_status\` — indexing status and health check
-- \`workspace_setup\` — bootstrap vexp config for a new project
-- \`submit_lsp_edges\` — submit type-resolved call edges (used by VS Code extension)
 - \`get_session_context\` — recall observations from current/previous sessions
-- \`search_memory\` — cross-session search for past decisions, insights, and explored code
-- \`save_observation\` — persist important insights with optional code symbol linking
-
-### Smart Features (automatic — no action needed)
-- **Intent Detection**: vexp auto-detects query intent from your prompt keywords.
-  "fix bug" → Debug mode (follows error paths), "refactor" → blast-radius mode,
-  "add feature" → Modify mode, default → Read mode. Each mode optimizes result ranking.
-- **Hybrid Search**: combines keyword matching (FTS) + semantic similarity (TF-IDF) + graph
-  centrality for better results. Finds \`validateCredentials\` when searching "authentication".
-- **Session Memory**: every tool call is auto-captured as an observation. Relevant memories
-  from previous sessions are auto-surfaced inside \`get_context_capsule\` results. Observations
-  linked to code symbols are auto-flagged stale when that code changes.
-- **Feedback Loop**: repeated queries with similar terms auto-expand the result budget.
-- **LSP Bridge**: VS Code captures type-resolved call edges for high-confidence call graphs.
-- **Change Coupling**: files modified together in git history are included as related context.
-- **Context Lineage**: frequently modified code gets a boost in relevance ranking.
+- \`search_memory\` — cross-session search for past decisions
+- \`save_observation\` — persist insights (prefer using run_pipeline's observation param instead)
 
 ### Workflow
-1. \`get_context_capsule("your task or question")\` — ALWAYS FIRST (includes relevant memories)
-2. Read the pivot files returned (full content)
-3. Review supporting skeletons for broader context
-4. Make targeted changes based on the context
-5. \`get_impact_graph\` before refactoring to verify no regressions
-6. \`save_observation\` to persist important decisions with code symbol links
-7. \`search_memory\` or \`get_session_context\` to recall past work
+1. \`run_pipeline("your task")\` — ALWAYS FIRST. Returns pivots + impact + memories in 1 call
+2. Make targeted changes based on the context returned
+3. \`run_pipeline\` again ONLY if you need more context during implementation
+4. Do NOT chain multiple vexp calls — one \`run_pipeline\` replaces capsule + impact + memory + observation
+
+### Smart Features (automatic — no action needed)
+- **Intent Detection**: auto-detects from your task keywords. "fix bug" → Debug, "refactor" → blast-radius, "add" → Modify
+- **Hybrid Search**: keyword + semantic + graph centrality ranking
+- **Session Memory**: auto-captures observations; memories auto-surfaced in results
+- **LSP Bridge**: VS Code captures type-resolved call edges
+- **Change Coupling**: co-changed files included as related context
 
 ### Advanced Parameters
-- \`include_tests: true\` — include test files (useful for debugging)
-- \`max_tokens: 12000\` — increase token budget for complex tasks
-- \`pivot_depth: 3\` — deeper graph traversal for broad exploration
-- \`skeleton_detail: "detailed"\` — more verbose skeletons
+- \`preset: "debug"\` — forces debug mode (capsule+tests+impact+memory)
+- \`preset: "refactor"\` — deep impact analysis (depth 5)
+- \`max_tokens: 12000\` — increase total budget for complex tasks
+- \`include_tests: true\` — include test files in results
+- \`include_file_content: false\` — omit full file content (lighter response)
 
 ### Multi-Repo Workspaces
-When multiple repos are indexed (monorepos, frontend+backend, microservices):
-- \`get_context_capsule\` queries **all repos** automatically — results show repo alias per file
-- Use \`repos: ["alias"]\` to restrict queries to specific repos
-- Use \`cross_repo: true\` on \`get_impact_graph\` and \`search_logic_flow\` to trace across repo boundaries
-- Use \`index_status\` to discover available repo aliases
-- \`get_skeleton\` accepts \`repo: "alias"\` to target a specific repo's files
+\`run_pipeline\` auto-queries all indexed repos. Use \`repos: ["alias"]\` to scope.
+Use \`index_status\` to discover available repo aliases.
 <!-- /vexp -->`;
 }
 function cursorTemplate(vars) {
     return `## vexp rules for Cursor <!-- vexp v${vars.version} -->
 
-**MANDATORY: use vexp MCP tools for ALL file analysis.**
-Do NOT use grep, glob, search, or file reads to explore the codebase.
-Use vexp MCP tools instead — they return pre-indexed, relevant context.
+**MANDATORY: use \`run_pipeline\` — do NOT grep, glob, or read files manually.**
+vexp returns pre-indexed, graph-ranked context in a single call.
 
 ### Workflow
-1. \`get_context_capsule\` with your task description — ALWAYS FIRST
-2. Review the provided pivot files and skeletons
-3. Make targeted changes based on the context
-4. \`get_impact_graph\` before refactoring exported symbols
+1. \`run_pipeline\` with your task description — ALWAYS FIRST (replaces all other tools)
+2. Make targeted changes based on the context returned
+3. \`run_pipeline\` again only if you need more context
 
 ### Available MCP tools
-- \`get_context_capsule\` — most relevant code (ALWAYS FIRST). Auto-detects intent: "fix bug" → debug mode, "refactor" → blast-radius mode
-- \`get_impact_graph\` — what breaks if you change a symbol
+- \`run_pipeline\` — **PRIMARY TOOL**. Runs capsule + impact + memory in 1 call.
+  Auto-detects intent. Includes file content. Example: \`run_pipeline({ "task": "fix auth bug" })\`
+- \`get_context_capsule\` — lightweight, for simple questions only
+- \`get_impact_graph\` — impact analysis of a specific symbol
 - \`search_logic_flow\` — execution paths between functions
-- \`get_skeleton\` — token-efficient file structure
+- \`get_skeleton\` — compact file structure
 - \`index_status\` — indexing status
-- \`workspace_setup\` — bootstrap vexp config for a new project
-- \`get_session_context\` — recall observations from current/previous sessions
-- \`search_memory\` — cross-session search for past decisions and insights
-- \`save_observation\` — persist important insights with optional code symbol linking
+- \`get_session_context\` — recall observations from sessions
+- \`search_memory\` — cross-session search
+- \`save_observation\` — persist insights (prefer run_pipeline's observation param)
 
 ### Tips
-- vexp uses hybrid search (keywords + semantic similarity + graph centrality) — natural language queries work well
-- Add \`include_tests: true\` when debugging to include test files in results
-- Repeated queries auto-expand result budget via feedback loop
-- Session memory auto-captures observations; use \`save_observation\` for important decisions
+- Natural language queries work well — vexp uses hybrid search (keyword + semantic + graph)
+- Add \`include_tests: true\` when debugging
+- Use \`preset: "refactor"\` for deep impact analysis
 
 ### Multi-Repo
-\`get_context_capsule\` auto-queries all indexed repos. Use \`repos: ["alias"]\` to scope, \`cross_repo: true\` on \`get_impact_graph\`/\`search_logic_flow\` to trace across repos. Run \`index_status\` to see available aliases.
+\`run_pipeline\` auto-queries all indexed repos. Use \`repos: ["alias"]\` to scope. Run \`index_status\` to see aliases.
 
 > **Tip:** To avoid confirmation prompts on every tool call, enable Yolo mode:
 > Cursor Settings → Features → Agent → Enable Yolo Mode.
@@ -530,40 +537,31 @@ Use vexp MCP tools instead — they return pre-indexed, relevant context.
 function windsurfTemplate(vars) {
     return `## vexp for Windsurf <!-- vexp v${vars.version} -->
 
-**MANDATORY: use vexp MCP tools for ALL file analysis.**
-Do NOT use grep, glob, search, or file reads to explore the codebase.
-Use vexp MCP tools instead — they return pre-indexed, relevant context.
+**MANDATORY: use \`run_pipeline\` — do NOT grep, glob, or read files manually.**
+vexp returns pre-indexed, graph-ranked context in a single call.
 
 ### Workflow
-1. \`get_context_capsule\` — ALWAYS FIRST for any task or question
-2. Review pivot files and skeletons returned
-3. Make targeted changes based on the context
-4. \`get_impact_graph\` before refactoring exported symbols
+1. \`run_pipeline\` with your task description — ALWAYS FIRST (replaces all other tools)
+2. Make targeted changes based on the context returned
+3. \`run_pipeline\` again only if you need more context
 
 ### Available MCP tools
-- \`get_context_capsule\` — most relevant code (ALWAYS FIRST). Auto-detects intent from your query
-- \`get_impact_graph\` — what breaks if you change a symbol
+- \`run_pipeline\` — **PRIMARY TOOL**. Runs capsule + impact + memory in 1 call.
+  Auto-detects intent. Includes file content. Example: \`run_pipeline({ "task": "fix auth bug" })\`
+- \`get_context_capsule\` — lightweight, for simple questions only
+- \`get_impact_graph\` — impact analysis of a specific symbol
 - \`search_logic_flow\` — execution paths between functions
-- \`get_skeleton\` — token-efficient file structure
+- \`get_skeleton\` — compact file structure
 - \`index_status\` — indexing status
-- \`workspace_setup\` — bootstrap vexp config for a new project
-- \`get_session_context\` — recall observations from current/previous sessions
-- \`search_memory\` — cross-session search for past decisions and insights
-- \`save_observation\` — persist important insights with optional code symbol linking
+- \`get_session_context\` — recall observations from sessions
+- \`search_memory\` — cross-session search
+- \`save_observation\` — persist insights (prefer run_pipeline's observation param)
 
-### Smart Features (automatic)
-- **Intent Detection**: "fix bug" → debug mode, "refactor" → blast-radius, "add" → modify
-- **Hybrid Search**: keyword + semantic + graph centrality ranking
-- **Session Memory**: auto-captures observations; use \`save_observation\` for important decisions
-- **Feedback Loop**: repeated queries auto-expand result budget
+### Smart Features
+Intent auto-detection, hybrid ranking, session memory, auto-expanding budget.
 
-### Multi-Repo Workspaces
-When multiple repos are indexed (monorepos, frontend+backend, microservices):
-- \`get_context_capsule\` queries **all repos** automatically — results show repo alias per file
-- Use \`repos: ["alias"]\` to restrict queries to specific repos
-- Use \`cross_repo: true\` on \`get_impact_graph\` and \`search_logic_flow\` to trace across repo boundaries
-- Use \`index_status\` to discover available repo aliases
-- \`get_skeleton\` accepts \`repo: "alias"\` to target a specific repo's files
+### Multi-Repo
+\`run_pipeline\` auto-queries all indexed repos. Use \`repos: ["alias"]\` to scope. Run \`index_status\` to see aliases.
 <!-- /vexp -->`;
 }
 function continueTemplate(vars) {
@@ -571,8 +569,8 @@ function continueTemplate(vars) {
         customCommands: [
             {
                 name: "vexp-context",
-                description: "Get vexp context capsule for current task",
-                prompt: "{{{ input }}}\n\nFirst, call get_context_capsule with the above task description.",
+                description: "Run vexp pipeline for current task",
+                prompt: "{{{ input }}}\n\nFirst, call run_pipeline with the above task description.",
             },
         ],
         mcpServers: [
@@ -588,204 +586,181 @@ function continueTemplate(vars) {
 function augmentTemplate(vars) {
     return `## vexp for Augment <!-- vexp v${vars.version} -->
 
-**MANDATORY: use vexp MCP tools for ALL file analysis.**
-Do NOT use grep, glob, search, or file reads to explore the codebase.
-Use vexp MCP tools instead — they return pre-indexed, relevant context.
+**MANDATORY: use \`run_pipeline\` — do NOT grep, glob, or read files manually.**
+vexp returns pre-indexed, graph-ranked context in a single call.
 
 When working on this codebase:
-1. Start every task by calling \`get_context_capsule\` — ALWAYS FIRST
-2. The capsule provides full content of pivot files + skeletons of related files
-3. Use \`get_impact_graph\` before refactoring exported symbols
+1. \`run_pipeline\` with task description — ALWAYS FIRST
+2. Make targeted changes based on the context returned
+3. \`run_pipeline\` again only if you need more context
 
 ### Available MCP tools
-- \`get_context_capsule\` — most relevant code (ALWAYS FIRST). Auto-detects intent from your query
-- \`get_impact_graph\` — what breaks if you change a symbol
+- \`run_pipeline\` — **PRIMARY TOOL**. Runs capsule + impact + memory in 1 call.
+  Example: \`run_pipeline({ "task": "fix auth bug" })\`
+- \`get_context_capsule\` — lightweight, for simple questions only
+- \`get_impact_graph\` — standalone impact analysis
 - \`search_logic_flow\` — execution paths between functions
 - \`get_skeleton\` — token-efficient file structure
 - \`index_status\` — indexing status
-- \`workspace_setup\` — bootstrap vexp config for a new project
-- \`get_session_context\` — recall observations from current/previous sessions
-- \`search_memory\` — cross-session search for past decisions and insights
-- \`save_observation\` — persist important insights with optional code symbol linking
+- \`get_session_context\` — recall observations from sessions
+- \`search_memory\` — cross-session search
+- \`save_observation\` — persist insights (prefer run_pipeline's observation param)
 
 ### Smart Features
-vexp auto-detects query intent (debug/refactor/modify/read) and uses hybrid ranking
-(keyword + semantic + graph centrality). Session memory auto-captures observations.
-Repeated queries auto-expand result budget.
+Intent auto-detection, hybrid ranking, session memory, auto-expanding budget.
 
-### Multi-Repo Workspaces
-When multiple repos are indexed (monorepos, frontend+backend, microservices):
-- \`get_context_capsule\` queries **all repos** automatically — results show repo alias per file
-- Use \`repos: ["alias"]\` to restrict queries to specific repos
-- Use \`cross_repo: true\` on \`get_impact_graph\` and \`search_logic_flow\` to trace across repo boundaries
-- Use \`index_status\` to discover available repo aliases
-- \`get_skeleton\` accepts \`repo: "alias"\` to target a specific repo's files
+### Multi-Repo
+\`run_pipeline\` auto-queries all indexed repos. Use \`repos: ["alias"]\` to scope. Run \`index_status\` to see aliases.
 <!-- /vexp -->`;
 }
 function copilotTemplate(vars) {
     return `## vexp context tools <!-- vexp v${vars.version} -->
 
-**MANDATORY: use vexp MCP tools for ALL file analysis.**
-Do NOT use grep, glob, search, or file reads to explore the codebase.
-Use vexp MCP tools instead — they return pre-indexed, relevant context.
+**MANDATORY: use \`run_pipeline\` — do NOT grep, glob, or read files manually.**
+vexp returns pre-indexed, graph-ranked context in a single call.
 
 ### Workflow
-1. \`get_context_capsule\` — ALWAYS FIRST for every task or question
-2. Review the provided pivot files and skeletons
-3. Make targeted changes based on the context
-4. \`get_impact_graph\` before refactoring exported symbols
+1. \`run_pipeline\` with your task description — ALWAYS FIRST (replaces all other tools)
+2. Make targeted changes based on the context returned
+3. \`run_pipeline\` again only if you need more context
 
 ### Available MCP tools
-- \`get_context_capsule\` — most relevant code (ALWAYS FIRST). Auto-detects intent from your query
-- \`get_impact_graph\` — shows which symbols depend on a given function/class
-- \`search_logic_flow\` — traces execution paths between functions
-- \`get_skeleton\` — token-efficient structural overview of a file
+- \`run_pipeline\` — **PRIMARY TOOL**. Runs capsule + impact + memory in 1 call.
+  Auto-detects intent. Includes file content. Example: \`run_pipeline({ "task": "fix auth bug" })\`
+- \`get_context_capsule\` — lightweight, for simple questions only
+- \`get_impact_graph\` — impact analysis of a specific symbol
+- \`search_logic_flow\` — execution paths between functions
+- \`get_skeleton\` — compact file structure
 - \`index_status\` — indexing status
-- \`workspace_setup\` — bootstrap vexp config for a new project
-- \`get_session_context\` — recall observations from current/previous sessions
-- \`search_memory\` — cross-session search for past decisions and insights
-- \`save_observation\` — persist important insights with optional code symbol linking
+- \`get_session_context\` — recall observations from sessions
+- \`search_memory\` — cross-session search
+- \`save_observation\` — persist insights (prefer run_pipeline's observation param)
 
 ### Smart Features
-vexp auto-detects query intent (debug/refactor/modify/read) and uses hybrid ranking
-(keyword + semantic + graph centrality). Session memory auto-captures observations.
-Repeated queries auto-expand result budget.
+Intent auto-detection, hybrid ranking, session memory, auto-expanding budget.
 
 ### Multi-Repo
-\`get_context_capsule\` auto-queries all indexed repos. Use \`repos: ["alias"]\` to scope, \`cross_repo: true\` on \`get_impact_graph\`/\`search_logic_flow\` to trace across repos. Run \`index_status\` to see available aliases.
+\`run_pipeline\` auto-queries all indexed repos. Use \`repos: ["alias"]\` to scope. Run \`index_status\` to see aliases.
 <!-- /vexp -->`;
 }
 function zedTemplate(vars) {
     return `## vexp for Zed <!-- vexp v${vars.version} -->
 
-**MANDATORY: use vexp MCP tools for ALL file analysis.**
-Do NOT use grep, glob, search, or file reads to explore the codebase.
-Use vexp MCP tools instead — they return pre-indexed, relevant context.
+**MANDATORY: use \`run_pipeline\` — do NOT grep, glob, or read files manually.**
+vexp returns pre-indexed, graph-ranked context in a single call.
 
 ### Workflow
-1. \`get_context_capsule\` — ALWAYS FIRST for any task or question
-2. Review pivot files and skeletons returned
-3. Make targeted changes based on the context
-4. \`get_impact_graph\` before refactoring exported symbols
+1. \`run_pipeline\` with your task description — ALWAYS FIRST (replaces all other tools)
+2. Make targeted changes based on the context returned
+3. \`run_pipeline\` again only if you need more context
 
 ### Available MCP tools
-- \`get_context_capsule\` — most relevant code (ALWAYS FIRST). Auto-detects intent from your query
-- \`get_impact_graph\` — dependency impact of a symbol change
+- \`run_pipeline\` — **PRIMARY TOOL**. Runs capsule + impact + memory in 1 call.
+  Example: \`run_pipeline({ "task": "fix auth bug" })\`
+- \`get_context_capsule\` — lightweight, for simple questions only
+- \`get_impact_graph\` — impact analysis of a specific symbol
 - \`search_logic_flow\` — execution paths between functions
-- \`get_skeleton\` — compact structural view of a file
+- \`get_skeleton\` — compact file structure
 - \`index_status\` — indexing status
-- \`workspace_setup\` — bootstrap vexp config for a new project
-- \`get_session_context\` — recall observations from current/previous sessions
-- \`search_memory\` — cross-session search for past decisions and insights
-- \`save_observation\` — persist important insights with optional code symbol linking
+- \`get_session_context\` — recall observations from sessions
+- \`search_memory\` — cross-session search
+- \`save_observation\` — persist insights (prefer run_pipeline's observation param)
 
 ### Smart Features
-vexp auto-detects query intent (debug/refactor/modify/read) and uses hybrid ranking
-(keyword + semantic + graph centrality). Session memory auto-captures observations.
-Repeated queries auto-expand result budget.
+Intent auto-detection, hybrid ranking, session memory, auto-expanding budget.
 
 ### Multi-Repo
-\`get_context_capsule\` auto-queries all indexed repos. Use \`repos: ["alias"]\` to scope, \`cross_repo: true\` on \`get_impact_graph\`/\`search_logic_flow\` to trace across repos. Run \`index_status\` to see available aliases.
+\`run_pipeline\` auto-queries all indexed repos. Use \`repos: ["alias"]\` to scope. Run \`index_status\` to see aliases.
 <!-- /vexp -->`;
 }
 function agentsMdTemplate(vars) {
     return `## vexp <!-- vexp v${vars.version} -->
 
-**MANDATORY: use vexp MCP tools for ALL file analysis.**
-Do NOT use grep, glob, search, or file reads to explore the codebase.
-Use vexp MCP tools instead — they return pre-indexed, relevant context.
-
-Before any code change or question, call \`get_context_capsule\` with a description of your task.
-This provides the most relevant source files and their skeletons with minimal token usage.
+**MANDATORY: use \`run_pipeline\` — do NOT grep, glob, or Read files.**
+vexp returns pre-indexed, graph-ranked context in a single call.
 
 ### Workflow
-1. \`get_context_capsule\` — ALWAYS FIRST for any task or question
-2. Review the provided pivot files and skeletons
-3. Make targeted changes based on the context
-4. \`get_impact_graph\` before refactoring exported symbols
+1. \`run_pipeline\` with your task description — ALWAYS FIRST (replaces all other tools)
+2. Make targeted changes based on the context returned
+3. \`run_pipeline\` again only if you need more context
 
 ### Available MCP tools
-- \`get_context_capsule\` — most relevant code (ALWAYS FIRST). Auto-detects intent from your query
-- \`get_impact_graph\` — what breaks if you change a symbol
+- \`run_pipeline\` — **PRIMARY TOOL**. Runs capsule + impact + memory in 1 call.
+  Auto-detects intent. Includes file content. Example: \`run_pipeline({ "task": "fix auth bug" })\`
+- \`get_context_capsule\` — lightweight, for simple questions only
+- \`get_impact_graph\` — impact analysis of a specific symbol
 - \`search_logic_flow\` — execution paths between functions
-- \`get_skeleton\` — token-efficient file structure
+- \`get_skeleton\` — compact file structure
 - \`index_status\` — indexing status
-- \`workspace_setup\` — bootstrap vexp config for a new project
-- \`get_session_context\` — recall observations from current/previous sessions
-- \`search_memory\` — cross-session search for past decisions and insights
-- \`save_observation\` — persist important insights with optional code symbol linking
+- \`get_session_context\` — recall observations from sessions
+- \`search_memory\` — cross-session search
+- \`save_observation\` — persist insights (prefer run_pipeline's observation param)
 
 ### Smart Features
-vexp auto-detects query intent (debug/refactor/modify/read) and uses hybrid ranking
-(keyword + semantic + graph centrality). Session memory auto-captures observations.
-Repeated queries auto-expand result budget. Use \`include_tests: true\` when debugging.
+Intent auto-detection, hybrid ranking, session memory, auto-expanding budget.
 
 ### Multi-Repo
-\`get_context_capsule\` auto-queries all indexed repos. Use \`repos: ["alias"]\` to scope, \`cross_repo: true\` on \`get_impact_graph\`/\`search_logic_flow\` to trace across repos. Run \`index_status\` to see available aliases.
+\`run_pipeline\` auto-queries all indexed repos. Use \`repos: ["alias"]\` to scope. Run \`index_status\` to see aliases.
 <!-- /vexp -->`;
 }
 function kiroTemplate(vars) {
     return `# vexp steering <!-- vexp v${vars.version} -->
 
-**MANDATORY: use vexp MCP tools for ALL file analysis.**
-Do NOT use grep, glob, search, or file reads to explore the codebase.
-Use vexp MCP tools instead — they return pre-indexed, relevant context.
-
-Always start tasks by calling \`get_context_capsule\` with a description of what you need.
+**MANDATORY: use \`run_pipeline\` — do NOT grep, glob, or read files manually.**
+vexp returns pre-indexed, graph-ranked context in a single call.
 
 ## Workflow
-1. \`get_context_capsule\` — ALWAYS FIRST for any task or question
-2. Review the provided pivot files and skeletons
-3. Make targeted changes based on the context
-4. \`get_impact_graph\` before refactoring exported symbols
+1. \`run_pipeline\` with your task description — ALWAYS FIRST (replaces all other tools)
+2. Make targeted changes based on the context returned
+3. \`run_pipeline\` again only if you need more context
 
 ## Available vexp tools
-- \`get_context_capsule\` — most relevant code (ALWAYS FIRST). Auto-detects intent from your query
-- \`get_impact_graph\` — impact analysis before refactoring
+- \`run_pipeline\` — **PRIMARY TOOL**. Runs capsule + impact + memory in 1 call.
+  Example: \`run_pipeline({ "task": "fix auth bug" })\`
+- \`get_context_capsule\` — lightweight, for simple questions only
+- \`get_impact_graph\` — impact analysis of a specific symbol
 - \`search_logic_flow\` — trace execution paths
 - \`get_skeleton\` — compact file structure
 - \`index_status\` — indexing status
-- \`workspace_setup\` — bootstrap config for new projects
-- \`get_session_context\` — recall observations from current/previous sessions
-- \`search_memory\` — cross-session search for past decisions and insights
-- \`save_observation\` — persist important insights with optional code symbol linking
+- \`get_session_context\` — recall observations from sessions
+- \`search_memory\` — cross-session search
+- \`save_observation\` — persist insights (prefer run_pipeline's observation param)
 
 ## Smart Features
-Intent detection (debug/refactor/modify/read), hybrid search, session memory, auto-expanding budget on repeated queries.
+Intent auto-detection, hybrid ranking, session memory, auto-expanding budget.
 
 ## Multi-Repo
-\`get_context_capsule\` auto-queries all indexed repos. Use \`repos: ["alias"]\` to scope, \`cross_repo: true\` on impact/flow. Run \`index_status\` to see aliases.
+\`run_pipeline\` auto-queries all indexed repos. Use \`repos: ["alias"]\` to scope. Run \`index_status\` to see aliases.
 <!-- /vexp -->`;
 }
 function genericTemplate(vars) {
     return `## vexp <!-- vexp v${vars.version} -->
 
-**MANDATORY: use vexp MCP tools for ALL file analysis.**
-Do NOT use grep, glob, search, or file reads to explore the codebase.
-Use vexp MCP tools instead — they return pre-indexed, relevant context.
+**MANDATORY: use \`run_pipeline\` — do NOT grep, glob, or Read files.**
+vexp returns pre-indexed, graph-ranked context in a single call.
 
 ### Workflow
-1. \`get_context_capsule\` — ALWAYS FIRST for any task or question
-2. Review the provided pivot files and skeletons
-3. Make targeted changes based on the context
-4. \`get_impact_graph\` before refactoring exported symbols
+1. \`run_pipeline\` with your task description — ALWAYS FIRST (replaces all other tools)
+2. Make targeted changes based on the context returned
+3. \`run_pipeline\` again only if you need more context
 
 ### Available MCP tools
-- \`get_context_capsule\` — most relevant code (ALWAYS FIRST). Auto-detects intent from your query
-- \`get_impact_graph\` — what breaks if you change a symbol
+- \`run_pipeline\` — **PRIMARY TOOL**. Runs capsule + impact + memory in 1 call.
+  Example: \`run_pipeline({ "task": "fix auth bug" })\`
+- \`get_context_capsule\` — lightweight, for simple questions only
+- \`get_impact_graph\` — impact analysis of a specific symbol
 - \`search_logic_flow\` — execution paths between functions
-- \`get_skeleton\` — token-efficient file structure
+- \`get_skeleton\` — compact file structure
 - \`index_status\` — indexing status
-- \`workspace_setup\` — bootstrap vexp config for a new project
-- \`get_session_context\` — recall observations from current/previous sessions
-- \`search_memory\` — cross-session search for past decisions and insights
-- \`save_observation\` — persist important insights with optional code symbol linking
+- \`get_session_context\` — recall observations from sessions
+- \`search_memory\` — cross-session search
+- \`save_observation\` — persist insights (prefer run_pipeline's observation param)
 
 ### Smart Features
-Intent detection (debug/refactor/modify/read), hybrid search, session memory, auto-expanding budget on repeated queries.
+Intent auto-detection, hybrid ranking, session memory, auto-expanding budget.
 
 ### Multi-Repo
-\`get_context_capsule\` auto-queries all indexed repos. Use \`repos: ["alias"]\` to scope, \`cross_repo: true\` on impact/flow. Run \`index_status\` to see aliases.
+\`run_pipeline\` auto-queries all indexed repos. Use \`repos: ["alias"]\` to scope. Run \`index_status\` to see aliases.
 <!-- /vexp -->`;
 }
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