context-mcp-server 1.0.5 → 1.0.7

package/codegraph/server.py

@@ -4,8 +4,7 @@ codegraph/server.py — MCP server exposing codebase knowledge graph tools.
 
 Tools:
   codegraph_build   — scan project, extract AST nodes, build graph (local only, no API)
-  codegraph_query   — fetch details about any part of the codebase via natural language
-  codegraph_explain — look up a specific node: type, file, connections
+  codegraph_query   — structural question OR single-node lookup (or both); replaces codegraph_explain
   codegraph_report  — return full CODEGRAPH_REPORT.md
   codegraph_nodes   — list nodes of a given type
   codegraph_path    — shortest path between two concepts
@@ -56,36 +55,21 @@ TOOLS = [
     Tool(
         name="codegraph_query",
         description=(
-            "Fetch details about any part of the codebase using a natural language question. "
-            "Searches the knowledge graph — instant, no API call. "
-            "Use for: finding functions, classes, files, understanding what exists, "
-            "what a module contains, what calls what, what imports what. "
-            "NOT for: bug investigation or tracing unexpected behavior — read the file for that."
+            "Ask a structural question about the codebase OR look up a specific node by name — or both in one call. "
+            "Pass `question` for natural-language traversal: what calls X, what does module Y depend on. "
+            "Pass `node` for fast single-node lookup: returns type, file, depends_on, used_by. "
+            "Pass both to get node detail + surrounding graph context together. "
+            "Returns structured text within token_budget. Use before reading any files."
         ),
         inputSchema={
             "type": "object",
             "properties": {
                 "path":         {"type": "string", "description": "Project root"},
-                "question":     {"type": "string", "description": "Natural language question"},
+                "question":     {"type": "string", "description": "Natural language question about the codebase"},
+                "node":         {"type": "string", "description": "Node name or partial name to look up (type, file, deps, callers)"},
                 "token_budget": {"type": "integer", "description": "Max tokens in response (default 2000)"},
             },
-            "required": ["path", "question"],
-        },
-    ),
-    Tool(
-        name="codegraph_explain",
-        description=(
-            "Look up a specific function, class, or module by name — returns its type, file location, "
-            "and all direct connections (what it depends on, what uses it). "
-            "Use when you already know the name and want its full context in the graph."
-        ),
-        inputSchema={
-            "type": "object",
-            "properties": {
-                "path": {"type": "string", "description": "Project root"},
-                "node": {"type": "string", "description": "Node name or partial name"},
-            },
-            "required": ["path", "node"],
+            "required": ["path"],
         },
     ),
     Tool(
@@ -143,7 +127,7 @@ async def call_tool(name: str, arguments: dict):
 async def _dispatch(name: str, args: dict):
     if name == "codegraph_build":   return await _build(args)
     if name == "codegraph_query":   return await _query(args)
-    if name == "codegraph_explain": return await _explain(args)
+    if name == "codegraph_explain": return await _query(args)
     if name == "codegraph_report":  return await _report(args)
     if name == "codegraph_nodes":   return await _nodes(args)
     if name == "codegraph_path":    return await _path(args)
@@ -223,19 +207,8 @@ async def _build(args: dict) -> dict:
 
 # ── Query / Report / Nodes / Path ─────────────────────────────────────────────
 
-async def _query(args: dict) -> dict:
-    graph_dict = load_graph(args["path"])
-    if not graph_dict:
-        raise ValueError("No graph found. Run codegraph_build first.")
-    return graph_answer(args["question"], graph_dict, token_budget=args.get("token_budget", 2000))
-
-
-async def _explain(args: dict) -> dict:
-    graph_dict = load_graph(args["path"])
-    if not graph_dict:
-        raise ValueError("No graph found. Run codegraph_build first.")
-
-    query = args["node"].lower()
+def _explain_node(node_name: str, graph_dict: dict) -> dict:
+    query = node_name.lower()
     nodes = graph_dict.get("nodes", [])
     edges = graph_dict.get("edges", [])
 
@@ -244,8 +217,8 @@ async def _explain(args: dict) -> dict:
         match = next((n for n in nodes if query in n.get("name", "").lower()), None)
     if not match:
         candidates = [n["name"] for n in nodes if query in n.get("id", "").lower()]
-        return {"found": False, "query": args["node"],
-                "message": f"No node matching '{args['node']}'.",
+        return {"found": False, "query": node_name,
+                "message": f"No node matching '{node_name}'.",
                 "suggestions": candidates[:10]}
 
     nid = match["id"]
@@ -254,13 +227,13 @@ async def _explain(args: dict) -> dict:
         if e.get("from") == nid:
             t = next((n for n in nodes if n.get("id") == e.get("to")), None)
             depends_on.append({"name": t["name"] if t else e["to"],
-                               "file": t.get("file","") if t else "",
-                               "relation": e.get("relation","→")})
+                               "file": t.get("file", "") if t else "",
+                               "relation": e.get("relation", "→")})
         elif e.get("to") == nid:
             s = next((n for n in nodes if n.get("id") == e.get("from")), None)
             used_by.append({"name": s["name"] if s else e["from"],
-                            "file": s.get("file","") if s else "",
-                            "relation": e.get("relation","→")})
+                            "file": s.get("file", "") if s else "",
+                            "relation": e.get("relation", "→")})
 
     return {
         "found":       True,
@@ -270,10 +243,28 @@ async def _explain(args: dict) -> dict:
         "description": match.get("description") or None,
         "depends_on":  depends_on[:20],
         "used_by":     used_by[:20],
-        "hint": None,
     }
 
 
+async def _query(args: dict) -> dict:
+    graph_dict = load_graph(args["path"])
+    if not graph_dict:
+        raise ValueError("No graph found. Run codegraph_build first.")
+
+    question  = args.get("question")
+    node_name = args.get("node")
+
+    if not question and not node_name:
+        raise ValueError("Provide at least one of: question, node")
+
+    result = {}
+    if node_name:
+        result["node"] = _explain_node(node_name, graph_dict)
+    if question:
+        result["query"] = graph_answer(question, graph_dict, token_budget=args.get("token_budget", 2000))
+    return result
+
+
 async def _report(args: dict) -> dict:
     report_path = Path(args["path"]) / "codegraph-cache" / "CODEGRAPH_REPORT.md"
     if report_path.exists():

package/package.json

@@ -1,13 +1,14 @@
 {
   "name": "context-mcp-server",
-  "version": "1.0.5",
+  "version": "1.0.7",
   "description": "Persistent AI memory + codebase knowledge graph MCP server. Works across Claude Code, Cursor, Gemini CLI, Codex, Windsurf, VS Code Copilot, Claude.ai, and ChatGPT.",
   "type": "module",
   "bin": {
     "context-mcp": "./src/index.js",
     "context-mcp-server": "./src/index.js",
     "context-mcp-http": "./src/http.js",
-    "ctx": "./src/cli.js"
+    "ctx": "./src/cli.js",
+    "context": "./src/cli.js"
   },
   "scripts": {
     "mcp": "node src/index.js",

package/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "codegraph-mcp"
-version = "1.0.5"
+version = "1.0.7"
 description = "Codebase knowledge graph MCP server — AST extraction, graph queries, community detection"
 readme = "README.md"
 requires-python = ">=3.11"

package/src/cli.js

@@ -107,8 +107,8 @@ function printSection(title, meta = '') {
 function printUsage() {
   printBanner();
 
-  // Terminal commands (ctx ...)
-  printSection('Terminal commands', 'run from your shell');
+  // Terminal commands (ctx / context ...)
+  printSection('Terminal commands', 'run from your shell  (ctx … or context …)');
   const cmd = (c, desc) => console.log(`  ${accent(c.padEnd(40))} ${faint(desc)}`);
   cmd('ctx',                           'open interactive mode');
   cmd('ctx list [project]',            'list entries + discussions + graphs');
@@ -131,8 +131,8 @@ function printUsage() {
   cmd('ctx help',                      'show this screen');
   console.log('');
 
-  // Interactive mode commands (no ctx prefix)
-  printSection('Interactive mode', 'type these inside  ctx  (no "ctx" prefix)');
+  // Interactive mode commands (no prefix needed)
+  printSection('Interactive mode', 'type these inside the UI — no "ctx" prefix needed');
   const icmd = (c, desc) => console.log(`  ${accent(c.padEnd(40))} ${faint(desc)}`);
   icmd('list [project]',               'list entries');
   icmd('search <query>',               'search context');
@@ -186,7 +186,7 @@ function cmdList(args) {
 
   for (const projectName of projectNames) {
     const pData     = projects[projectName];
-    const graph     = allGraphs.find(g => g.path?.toLowerCase().includes(projectName.toLowerCase()));
+    const graph     = _graphForProject(allGraphs, projectName);
     const activeD   = pData.discussions.filter(d => d.status === 'active').length;
     const totalSecs = (pData.contexts.length > 0 ? 1 : 0) + (pData.discussions.length > 0 ? 1 : 0) + (graph ? 1 : 0);
     let   secIdx    = 0;
@@ -240,7 +240,7 @@ function cmdList(args) {
   }
 
   // Orphan graphs (no matching project)
-  const orphanGraphs = allGraphs.filter(g => !projectNames.some(p => g.path?.toLowerCase().includes(p.toLowerCase())));
+  const orphanGraphs = allGraphs.filter(g => !projectNames.some(p => _graphForProject([g], p)));
   if (orphanGraphs.length) {
     console.log(`\n  ${color(C.dblue, '◇')} ${muted('other graphs')}`);
     for (const g of orphanGraphs) {
@@ -292,7 +292,7 @@ function cmdProjects() {
     const entries   = getContext({ project: project.name, limit: 3, compact: true }).filter(e => e.status !== 'archived');
     const discs     = allDiscs.filter(d => (d.project || 'global') === project.name);
     const activeD   = discs.filter(d => d.status === 'active');
-    const graph     = graphs.find(g => g.path?.toLowerCase().includes(project.name.toLowerCase()));
+    const graph     = _graphForProject(graphs, project.name);
 
     const barLen = Math.min(Math.ceil(project.count / 2), 24);
     const bar    = color(C.dblue, '█'.repeat(barLen)) + color(C.darkgray, '░'.repeat(24 - barLen));
@@ -429,7 +429,7 @@ function cmdBenchmark() {
   printSection('Benchmark', 'real token savings');
 
   const RESUME_LIMIT = 15;
-  const COMPACT_AT   = 50;
+  const COMPACT_AT   = 20;
 
   // ── Measure entry sizes from actual stored data ──────────────────────────────
   const allEntries   = getContext({ limit: 500, compact: false });
@@ -567,6 +567,30 @@ const _GLOBAL_GITIGNORE_ENTRIES = [
   '.mcp.json',
 ];
 
+// Match a graph to a project by exact last-path-component comparison (not substring)
+function _graphForProject(graphs, projectName) {
+  const norm = p => (p || '').toLowerCase().replace(/\\/g, '/').replace(/\/$/, '');
+  const name = projectName.toLowerCase();
+  return graphs.find(g => norm(g.path).split('/').pop() === name) || null;
+}
+
+const _PROJECT_GITIGNORE_ENTRIES = [
+  '.claude/', '.cursor/', '.vscode/', '.gemini/', '.codex/',
+  'codegraph-cache/', '.mcp.json', 'CLAUDE.md', 'GEMINI.md', 'AGENTS.md',
+];
+
+function _updateProjectGitignore(projectDir) {
+  const giPath = join(projectDir, '.gitignore');
+  const existing = existsSync(giPath) ? readFileSync(giPath, 'utf8') : '';
+  const lines = existing.split(/\r?\n/);
+  const missing = _PROJECT_GITIGNORE_ENTRIES.filter(e => !lines.includes(e));
+  if (!missing.length) return;
+  const block = '\n# context-mcp — written by ctx install\n' + missing.join('\n') + '\n';
+  writeFileSync(giPath, (existing ? existing.trimEnd() : '') + block, 'utf8');
+  console.log(`  ${ok('✓')} ${'project .gitignore'.padEnd(28)} ${faint(giPath.replace(/\\/g, '/'))}`);
+  for (const e of missing) console.log(`      ${faint('+ ' + e)}`);
+}
+
 function _updateGlobalGitignore() {
   // Resolve global gitignore path: git config > ~/.gitignore_global > ~/.gitignore
   let giPath = null;
@@ -829,6 +853,9 @@ async function cmdInstall(args) {
   console.log(faint(`  ${keys.length} platform(s) installed  ·  scope: ${scope}  ·  ${destLabel}`));
   console.log('');
 
+  // ── Project .gitignore — add context-mcp entries for this project ──────────
+  _updateProjectGitignore(process.cwd());
+
   // ── Global gitignore — add context-mcp runtime files if global gitignore exists ──
   _updateGlobalGitignore();
   console.log('');

package/src/db.js

@@ -23,6 +23,11 @@ const PROJECTS_PATH     = join(DATA_DIR, 'projects.json');
 
 const MAX_CONTENT_LENGTH = 5000;
 const PREVIEW_LENGTH = 200;
+
+// Normalize file paths for cross-platform comparison (Windows case + slash variants)
+function normPath(p) {
+  return p ? p.toLowerCase().replace(/\\/g, '/').replace(/\/$/, '') : '';
+}
 const WRITE_DEBOUNCE_MS = 500;
 const LOCK_WAIT_TIMEOUT_MS = 2000;
 
@@ -126,9 +131,9 @@ function mergeStore(latest, local) {
     if (_changedDiscussionNames.has(disc.name)) discussionsByName.set(disc.name, disc);
   }
 
-  const graphsByPath = new Map((latest.graphs || []).map(g => [g.path, g]));
+  const graphsByPath = new Map((latest.graphs || []).map(g => [normPath(g.path), g]));
   for (const graph of (local.graphs || [])) {
-    if (_changedGraphPaths.has(graph.path)) graphsByPath.set(graph.path, graph);
+    if (_changedGraphPaths.has(graph.path)) graphsByPath.set(normPath(graph.path), graph);
   }
 
   const projectsById = new Map((latest.projects || []).map(p => [p.id, p]));
@@ -307,10 +312,15 @@ export function updateContext({ id, content, title, tags, type, status, files, c
  * @param {Object} opts
  * @param {boolean} opts.compact - If true, returns previews instead of full content (saves tokens)
  */
-export function getContext({ project, tags, limit = 20, compact = false } = {}) {
+export function getContext({ project, tags, limit = 20, compact = false, ids } = {}) {
   refreshFromDisk();
   const store = load();
   let results = store.contexts;
+  if (ids && ids.length) {
+    const idSet = new Set(ids);
+    results = results.filter(c => idSet.has(c.id));
+    return compact ? results.map(compactEntry) : results;
+  }
   if (project) results = results.filter(c => c.project === project || c.project === 'global');
   if (tags && tags.length) {
     const tagList = Array.isArray(tags) ? tags : tags.split(',').map(t => t.trim());
@@ -343,12 +353,14 @@ export function searchContext({ query, project, limit = 10, compact = false }) {
   return compact ? sliced.map(compactEntry) : sliced;
 }
 
-export function deleteContext({ id }) {
+export function deleteContext({ id, ids }) {
   refreshFromDisk();
   const store = load();
   const before = store.contexts.length;
-  const removed = store.contexts.filter(c => c.id === id);
-  store.contexts = store.contexts.filter(c => c.id !== id);
+  const idSet = new Set(ids && ids.length ? ids : (id ? [id] : []));
+  if (!idSet.size) return { deleted: 0 };
+  const removed = store.contexts.filter(c => idSet.has(c.id));
+  store.contexts = store.contexts.filter(c => !idSet.has(c.id));
   if (store.contexts.length < before) {
     for (const entry of removed) {
       _deletedContextIds.add(entry.id);
@@ -713,7 +725,7 @@ export function flushStore() { flushToDisk(); }
 
 // ── Auto-compaction ───────────────────────────────────────────────────────────
 
-const COMPACTION_THRESHOLD = 50;
+const COMPACTION_THRESHOLD = 20;
 const COMPACTION_TARGET = 30;
 
 export function shouldCompact(project) {
@@ -753,7 +765,14 @@ export function compactProject(project, summaryContent) {
 export function saveGraph({ path, nodes, edges, communities, cached, changed, time_ms, summary }) {
   refreshFromDisk();
   const store = load();
-  const existing = store.graphs.find(g => g.path === path);
+  // Deduplicate: collapse any case/slash variants of same path, keep newest
+  const dupes = store.graphs.filter(g => normPath(g.path) === normPath(path));
+  if (dupes.length > 1) {
+    const keep = dupes.reduce((a, b) => (a.builtAt >= b.builtAt ? a : b));
+    store.graphs = store.graphs.filter(g => normPath(g.path) !== normPath(path));
+    store.graphs.push(keep);
+  }
+  const existing = store.graphs.find(g => normPath(g.path) === normPath(path));
   const record = {
     path,
     nodes:       nodes       ?? existing?.nodes       ?? 0,
@@ -777,7 +796,7 @@ export function saveGraph({ path, nodes, edges, communities, cached, changed, ti
 
 export function getGraph(path) {
   const store = load();
-  if (path) return store.graphs.find(g => g.path === path) || null;
+  if (path) return store.graphs.find(g => normPath(g.path) === normPath(path)) || null;
   return store.graphs;
 }
 

package/src/hooks/autoContext.js

@@ -3,7 +3,7 @@ import { fireAutoLink } from './autoLink.js';
 
 export function saveAutoContext({ title, content, type, files, state, tags = [] }) {
   const entry = saveContext({
-    project:   state.sessionProject || 'global',
+    project:   state.sessionProject || null,
     sessionId: state.sessionId || null,
     title,
     content,

package/src/templates/CLAUDE.md

@@ -15,7 +15,12 @@ Every conversation starts with `context.resume`. Every codebase question uses `c
 
 ## 1. Start of Every Conversation (MANDATORY)
 
-Call `context` tool, `action: "resume"`, `project: "<project-name>"` **before anything else**.
+Call `context` tool **before anything else** with:
+- `action: "resume"`
+- `project: "<basename of git repo root dir>"` — infer from cwd if not stated
+- `rootPath: "<absolute path to git repo root>"` — required for sandbox + graph lookup
+
+Both fields are required: `project` names the memory bucket, `rootPath` enables exact graph matching and file sandboxing.
 
 Returns:
 - `recentEntries` — decisions, bugs, notes from previous conversations
@@ -34,7 +39,7 @@ Then:
 
 **After graph build or rebuild** — every time `codegraph_build` completes:
 ```
-context.save  type: "architecture"  title: "ContextGraph built — <project>"
+context.save  project: "<project>"  type: "architecture"  title: "ContextGraph built — <project>"
 content: "nodes: X | edges: Y | communities: Z"
 ```
 
@@ -59,7 +64,7 @@ Do NOT save: routine reads, search results, temporary debugging dead-ends.
 
 Feature spans multiple sessions → `discussion.create` or `discussion.update`.
 Need past info → `search` before asking user.
-Always pass `project`. Auto-compact fires at >50 entries.
+Always pass `project`. Auto-compact fires at >20 entries.
 
 ---
 

package/src/templates/commands/context-resume.md

@@ -1,4 +1,6 @@
-Call the `context` MCP tool with `action: "resume"` and `project: "$ARGUMENTS"` (if no argument given, infer the project name from the current working directory name).
+Call the `context` MCP tool with `action: "resume"`, `project: "$ARGUMENTS"` (if no argument given, infer the project name from the current working directory name), and `rootPath: "<absolute path to the project root / git repo root>"`.
+
+Both `project` and `rootPath` are required: `project` names the memory bucket, `rootPath` enables exact graph lookup and file sandboxing.
 
 This loads:
 - Recent decisions, bugs, and notes from past sessions

package/src/templates/skills/SKILL.md

@@ -18,9 +18,12 @@ Persistent memory + codebase knowledge graph across every conversation.
 
 ## MANDATORY: Start of Every Conversation
 
-Call `context` tool, `action: "resume"`, `project: "<project-name>"` **before any tool or response**.
+Call `context` tool **before any tool or response** with:
+- `action: "resume"`
+- `project: "<basename of git repo root dir>"` — infer from `cwd` if not stated
+- `rootPath: "<absolute path to git repo root>"` — required for sandbox + graph lookup
 
-Infer `project` from the working directory name if not stated.
+Both fields are required: `project` names the memory bucket, `rootPath` enables exact graph matching and file sandboxing.
 
 Returns:
 - `recentEntries` — decisions, bugs, notes from past sessions
@@ -40,7 +43,7 @@ Then:
 **1. After graph build or rebuild**
 Every time `codegraph_build` completes successfully, immediately call:
 ```
-context.save  type: "architecture"  title: "ContextGraph built — <project>"
+context.save  project: "<project>"  type: "architecture"  title: "ContextGraph built — <project>"
 content: "nodes: X | edges: Y | communities: Z | built: <timestamp>"
 ```
 
@@ -70,7 +73,7 @@ Do NOT save for: routine file reads, search results, explanations of existing co
 | Deploy / release step discovered | `note` |
 | Milestone / feature / task completed | `note` |
 
-Always pass `project`. Feature spans multiple sessions → `discussion.create` or `discussion.update`. Need past info → `search` before asking user. Auto-compact fires at >50 entries.
+Always pass `project`. Feature spans multiple sessions → `discussion.create` or `discussion.update`. Need past info → `search` before asking user. Auto-compact fires at >20 entries.
 
 ---
 
@@ -86,9 +89,8 @@ Parses codebase into AST graph via tree-sitter. Extracts functions, classes, imp
 
 ### Query (free, instant, forever)
 ```
-codegraph_query(path, question)   → find functions, classes, files, dependencies, callers
-codegraph_explain(path, node)     → one node: type, file, depends_on, used_by
-codegraph_path(path, from, to)    → shortest path between two concepts
+codegraph_query(path, question?, node?)  → structural question OR single-node lookup (or both in one call)
+codegraph_path(path, from, to)           → shortest path between two concepts
 codegraph_nodes(path, type)       → list all nodes of a type
 codegraph_report(path)            → god nodes, clusters, surprises
 ```

package/src/tools/codegraph.js

@@ -40,92 +40,23 @@ export const definitions = [
       required: ['path'],
     },
   },
-  {
-    name: 'codegraph_extract',
-    description:
-      'Return raw content of changed code and doc/PDF files so the AI can write descriptions. ' +
-      'Code files: lists existing AST nodes — AI writes a description for each. ' +
-      'Doc files: AI extracts new concept nodes. ' +
-      'Call after codegraph_build, then call codegraph_add_nodes with results. ' +
-      'Pass force:true to re-enrich all files (not just changed ones).',
-    inputSchema: {
-      type: 'object',
-      properties: {
-        path:  { type: 'string', description: 'Project root (same as codegraph_build)' },
-        limit: { type: 'integer', description: 'Max files to return per call (default 10)' },
-        force: { type: 'boolean', description: 'Return all files, not just changed (for re-enrichment)' },
-      },
-      required: ['path'],
-    },
-  },
-  {
-    name: 'codegraph_add_nodes',
-    description:
-      'Add concept nodes extracted by the AI into the graph. ' +
-      'Call after reading codegraph_extract output. ' +
-      'Each node: name, type, file, and optionally description and relations.',
-    inputSchema: {
-      type: 'object',
-      properties: {
-        path:  { type: 'string', description: 'Project root' },
-        nodes: {
-          type: 'array',
-          description: 'Concept nodes to add',
-          items: {
-            type: 'object',
-            properties: {
-              name:        { type: 'string' },
-              type:        { type: 'string', description: 'class|function|concept|service|decision|requirement' },
-              file:        { type: 'string', description: 'Relative file path this concept came from' },
-              description: { type: 'string' },
-              relations: {
-                type: 'array',
-                items: {
-                  type: 'object',
-                  properties: {
-                    name:     { type: 'string' },
-                    relation: { type: 'string', description: 'depends-on|uses|implements|defines|documents' },
-                  },
-                },
-              },
-            },
-            required: ['name', 'type', 'file'],
-          },
-        },
-      },
-      required: ['path', 'nodes'],
-    },
-  },
   {
     name: 'codegraph_query',
     description:
-      'Ask a structural/dependency question about the codebase. ' +
-      'Pure graph traversal — returns NODE/EDGE structured text truncated to token_budget. ' +
-      'Good for: "what does module X depend on?", "what calls function Y?", "what is the path from A to B?". ' +
-      'NOT for: bug investigation, logic errors, or understanding what code actually does — read the file directly for those.',
+      'Ask a structural question about the codebase OR look up a specific node by name — or both in one call. ' +
+      'Pass `question` for natural-language traversal: "what does module X depend on?", "what calls function Y?". ' +
+      'Pass `node` for fast single-node lookup: returns type, file, depends_on, used_by. ' +
+      'Pass both to get node detail + surrounding graph context together. ' +
+      'Returns structured text within token_budget. Use before reading any files.',
     inputSchema: {
       type: 'object',
       properties: {
         path:         { type: 'string', description: 'Project root' },
-        question:     { type: 'string', description: 'Natural language question' },
+        question:     { type: 'string', description: 'Natural language question about the codebase' },
+        node:         { type: 'string', description: 'Node name or partial name to look up (type, file, deps, callers)' },
         token_budget: { type: 'integer', description: 'Max tokens in response (default 2000)' },
       },
-      required: ['path', 'question'],
-    },
-  },
-  {
-    name: 'codegraph_explain',
-    description:
-      'Look up a node by name — returns description, type, file, and direct neighbors (depends_on + used_by). ' +
-      'Use to understand what a specific function/class/module does and how it connects. ' +
-      'Descriptions are AI-written via codegraph_add_nodes.',
-    inputSchema: {
-      type: 'object',
-      properties: {
-        path: { type: 'string', description: 'Project root' },
-        node: { type: 'string', description: 'Node name or partial name' },
-      },
-      required: ['path', 'node'],
+      required: ['path'],
     },
   },
   {
@@ -184,7 +115,10 @@ export function handle(name, args, state) {
         summary:     result.summary || '',
       });
 
-      const project = state?.sessionProject || 'global';
+      const inferredProject = args.path
+        ? args.path.replace(/\\/g, '/').replace(/\/$/, '').split('/').pop()
+        : null;
+      const project = state?.sessionProject || inferredProject || null;
       const title   = `CodeGraph — ${args.path}`;
       const content = [
         `nodes: ${result.nodes} | edges: ${result.edges} | communities: ${result.communities}`,

package/src/tools/context.js

@@ -28,9 +28,9 @@ export const definition = {
     `Factual memory — record what happened, what was decided, what broke, what was built.\n` +
     `• "resume"       — START HERE every conversation. Loads recent context, active discussions, and graph status for a project.\n` +
     `• "save"         — Store a note, decision, bug, or code snippet. Auto-deduplicates.\n` +
-    `• "get"          — Load recent entries (compact previews). Auto-digests when large.\n` +
+    `• "get"          — Load entries. Pass id/ids to fetch specific ones, or project/tags/limit for recent.\n` +
     `• "update"       — Edit an existing entry by id (any field).\n` +
-    `• "delete"       — Remove an entry by id.\n` +
+    `• "delete"       — Remove one entry (id) or multiple at once (ids: [...]).\n` +
     `• "list_projects"— Show all projects and entry counts.`,
   inputSchema: {
     type: 'object',
@@ -50,7 +50,8 @@ export const definition = {
       expiresAt:     { type: 'string' },
       limit:         { type: 'number' },
       includeArchived: { type: 'boolean' },
-      id:            { type: 'string' },
+      id:            { type: 'string', description: 'Single entry ID (get/update/delete)' },
+      ids:           { type: 'array', items: { type: 'string' }, description: 'Multiple entry IDs — fetch or delete several at once' },
     },
     required: ['action'],
   },
@@ -92,9 +93,15 @@ export async function handle(args, state) {
         .filter(e => e.status !== 'archived');
       const discussions   = listDiscussions({ project: proj, status: 'active' });
       const allGraphs     = listGraphs();
-      const graph         = proj
-        ? allGraphs.find(g => g.path?.toLowerCase().includes(proj.toLowerCase())) || allGraphs[0] || null
-        : allGraphs[0] || null;
+      const np = p => (p || '').toLowerCase().replace(/\\/g, '/');
+      const graph         = resolvedRoot
+        ? allGraphs.find(g => np(g.path) === np(resolvedRoot)) || null
+        : proj
+          ? allGraphs.find(g => {
+              const parts = np(g.path).split('/');
+              return parts[parts.length - 1] === proj.toLowerCase();
+            }) || null
+          : null;
       const totalEntries  = countContext(proj);
 
       // Auto-restore single active discussion
@@ -183,8 +190,20 @@ export async function handle(args, state) {
 
     case 'get': {
       if (!args.project && state.sessionProject) args = { ...args, project: state.sessionProject };
-      archiveExpired(args.project);
       const includeArchived = args.includeArchived === true;
+
+      // Fetch by specific ID(s) — bypass project/tag/limit filters
+      const ids = args.ids || (args.id ? [args.id] : null);
+      if (ids) {
+        const entries = getContext({ ids, compact: false })
+          .filter(e => includeArchived || e.status !== 'archived');
+        return {
+          entries, count: entries.length,
+          message: entries.length ? `Found ${entries.length} entries.` : 'No entries found for given IDs.',
+        };
+      }
+
+      archiveExpired(args.project);
       let entries = getContext({ project: args.project, tags: args.tags, limit: args.limit, compact: true });
       if (!includeArchived) entries = entries.filter(e => e.status !== 'archived');
       const fullEntries = entries.length > 10
@@ -210,8 +229,9 @@ export async function handle(args, state) {
     }
 
     case 'delete': {
-      if (!args.id) throw new Error('id is required for delete');
-      return deleteContext(args);
+      if (!args.id && !args.ids) throw new Error('id or ids is required for delete');
+      const result = deleteContext(args);
+      return { ...result, message: `Deleted ${result.deleted} entr${result.deleted === 1 ? 'y' : 'ies'}.` };
     }
 
     case 'list_projects': {