context-mcp-server 1.1.1 → 1.1.3

package/README.md

@@ -11,7 +11,7 @@
 
 Persistent memory and codebase knowledge graph for AI coding assistants — delivered as a single MCP server.
 
-One shared context store across Claude Code, Cursor, Gemini CLI, Codex, Windsurf, VS Code Copilot, Antigravity IDE, Claude.ai, and ChatGPT. Save context from one AI, pick it up in another.
+One shared context store across Claude Code, Cursor, Gemini CLI, Codex, Windsurf, VS Code Copilot, Claude.ai, and ChatGPT. Save context from one AI, pick it up in another.
 
 ---
 
@@ -77,8 +77,7 @@ ctx install --cursor      # Cursor
 ctx install --vscode      # VS Code Copilot
 ctx install --gemini      # Gemini CLI
 ctx install --codex       # Codex CLI
-ctx install --windsurf      # Windsurf
-ctx install --antigravity   # Antigravity IDE
+ctx install --windsurf    # Windsurf
 ```
 
 For Codex project installs, `ctx install --codex` writes:

package/codegraph/callflow_html.py

@@ -210,7 +210,7 @@ def to_html(graph_dict: dict, output_path: str) -> str:
 <p>{len(nodes)} nodes · {len(edges)} edges · {len(communities)} communities · generated {escape(generated)}</p>
 {god_html}
 <div class="mermaid">
-{escape(overview_mermaid)}
+{overview_mermaid}
 </div>
 </section>"""
 
@@ -239,7 +239,7 @@ def to_html(graph_dict: dict, output_path: str) -> str:
   <div class="card"><h3>Key Files</h3><ul>{files_html}</ul></div>
 </div>
 <div class="mermaid">
-{escape(diagram)}
+{diagram}
 </div>
 {"<h3>Incoming Cross-Community Calls</h3>" + table if table else ""}
 <hr>

package/codegraph/export.py

@@ -416,7 +416,7 @@ def to_obsidian(graph_dict: dict, output_dir: str) -> str:
         fpath = n.get("file", "")
         ntype = n.get("type", "")
         comm  = node_community.get(nid)
-        comm_tag = _obsidian_tag(comm["label"]) if comm else "misc"
+        comm_tag = _obsidian_tag(comm.get("label", f"community_{comm['id']}")) if comm else "misc"
 
         lines = [
             "---",

package/codegraph/extractors/ast_extractor.py

@@ -530,8 +530,10 @@ def _extract_with_regex(source: str, rel_path: str, ext: str) -> list[dict]:
                         "imports": import_names[:],
                     })
 
+    # brace-scope tracking only works for brace-delimited languages
+    _BRACE_LANGS = {"javascript", "typescript", "go", "rust", "java", "c", "cpp", "csharp", "php", "swift"}
     func_nodes = [n for n in nodes if n["type"] == "function"]
-    if func_nodes:
+    if func_nodes and lang in _BRACE_LANGS:
         _attach_calls_brace(lines, func_nodes)
 
     return nodes

package/codegraph/graph/builder.py

@@ -25,44 +25,48 @@ def build(all_nodes: list[dict]) -> "nx.DiGraph | dict":
 
     G = nx.DiGraph()
 
-    node_by_name: dict[str, str] = {}    # name -> id
-    module_by_file: dict[str, str] = {}  # rel_path -> module node id
+    _name_to_ids: dict[str, list[str]] = {}  # name -> [ids] (may be multiple)
+    file_rep: dict[str, str] = {}            # rel_path -> representative node id (module > file > first)
+    file_imports: dict[str, list[str]] = {}  # rel_path -> aggregated import names
 
     for node in all_nodes:
         nid = node.get("id", "")
         if not nid:
             continue
         G.add_node(nid, **{k: v for k, v in node.items() if k not in ("imports", "calls", "relations")})
-        node_by_name[node.get("name", "")] = nid
-        if node.get("type") == "module":
-            module_by_file[node.get("file", "")] = nid
+        name = node.get("name", "")
+        if name:
+            _name_to_ids.setdefault(name, []).append(nid)
+        # Track a representative node per file (prefer module, then file, then first seen)
+        frel = node.get("file", "")
+        ntype = node.get("type", "")
+        if frel and (frel not in file_rep or ntype in ("module", "file")):
+            file_rep[frel] = nid
+        # Aggregate imports per file from any node type
+        for imp in node.get("imports", []):
+            lst = file_imports.setdefault(frel, [])
+            if imp not in lst:
+                lst.append(imp)
+
+    # Unambiguous name→id map: only include names that resolve to exactly one node
+    node_by_name: dict[str, str] = {n: ids[0] for n, ids in _name_to_ids.items() if len(ids) == 1}
 
-    # Build file-path lookup from module nodes
+    # Build file-path lookup from all file/module representative nodes
     file_node: dict[str, str] = {}
-    for rel_path, mod_id in module_by_file.items():
+    for rel_path, rep_id in file_rep.items():
         p = rel_path.replace("\\", "/")
         stem = p.split("/")[-1].split(".")[0]
         base = p.split("/")[-1]
         for key in (stem, base, p):
-            file_node.setdefault(key, mod_id)
-
-    # defined-in edges: child nodes → their module
-    for node in all_nodes:
-        nid = node.get("id", "")
-        for rel in node.get("relations", []):
-            target_id = rel.get("id") or node_by_name.get(rel.get("name", ""))
-            if target_id and target_id != nid:
-                G.add_edge(nid, target_id,
-                           relation=rel.get("relation", "relates-to"),
-                           confidence=rel.get("confidence", "EXTRACTED"))
+            file_node.setdefault(key, rep_id)
 
-    # Import edges: module → module
+    # Import edges: file → file (aggregated from all node types per file)
     seen_edges: set[tuple] = set()
-    for node in all_nodes:
-        if node.get("type") != "module":
+    for frel, imports in file_imports.items():
+        src_id = file_rep.get(frel)
+        if not src_id:
             continue
-        src_id = node.get("id", "")
-        for imp in node.get("imports", []):
+        for imp in imports:
             clean = imp.lstrip(".")
             parts = clean.replace("\\", "/").split("/")
             last  = parts[-1]

package/codegraph/graph/clustering.py

@@ -64,8 +64,9 @@ def _partition(G: nx.Graph, resolution: float = 1.0) -> dict[str, int]:
     except ImportError:
         pass
 
-    kwargs = {"seed": 42, "threshold": 1e-4, "resolution": resolution}
-    if "max_level" in inspect.signature(nx.community.louvain_communities).parameters:
+    louvain_sig = inspect.signature(nx.community.louvain_communities).parameters
+    kwargs = {"seed": 42, "resolution": resolution}
+    if "max_level" in louvain_sig:
         kwargs["max_level"] = 10
     communities = nx.community.louvain_communities(stable, **kwargs)
     return {node: cid for cid, nodes in enumerate(communities) for node in nodes}
@@ -102,7 +103,8 @@ def cluster(
     if exclude_hubs_percentile is not None:
         degrees = sorted(d for _, d in G.degree())
         if degrees:
-            idx = max(0, int(len(degrees) * exclude_hubs_percentile / 100) - 1)
+            # idx is the last position we keep; nodes beyond this are hubs
+            idx = min(len(degrees) - 1, int(len(degrees) * exclude_hubs_percentile / 100))
             threshold = degrees[idx]
             hub_nodes = {n for n, d in G.degree() if d > threshold}
 

package/codegraph/graph/query.py

@@ -5,6 +5,7 @@ No LLM call on query — pure graph + keyword matching.
 """
 
 import re
+from collections import deque
 from typing import Any
 
 
@@ -114,10 +115,10 @@ def _find_by_name(nodes: list, name: str) -> dict | None:
 
 
 def _detect_intent(q: str) -> str:
-    if any(w in q for w in ("depend", "import", "use", "require")):
-        return "depends_on"
     if any(w in q for w in ("used by", "who calls", "caller")):
         return "used_by"
+    if any(w in q for w in ("depend", "import", "use", "require")):
+        return "depends_on"
     if any(w in q for w in ("path", "connect", "relate", "between")):
         return "path"
     if any(w in q for w in ("list", "all", "show all", "every")):
@@ -164,9 +165,9 @@ def _shortest_path(from_node: dict, to_node: dict, edges: list, nodes: list) ->
 
     start, end = from_node["id"], to_node["id"]
     visited = {start: None}
-    queue = [start]
+    queue: deque[str] = deque([start])
     while queue:
-        cur = queue.pop(0)
+        cur = queue.popleft()
         if cur == end:
             break
         for nb in adj.get(cur, []):

package/codegraph/graph/symbol_resolution.py

@@ -79,11 +79,14 @@ def resolve_calls(
                 continue
 
             target_ids: list[str] = []
+            via_import = False
 
             # 1. Try (imported_module_stem, callee_name) for import-guided resolution
             for stem in imported_stems:
                 candidates = module_index.get((stem, callee_name), [])
                 target_ids.extend(candidates)
+            if target_ids:
+                via_import = True
 
             # 2. Fall back to global unique name match
             if not target_ids:
@@ -101,7 +104,7 @@ def resolve_calls(
                 continue
 
             existing_edge_keys.add(key)
-            confidence = "EXTRACTED" if imported_stems else "INFERRED"
+            confidence = "EXTRACTED" if via_import else "INFERRED"
             new_edges.append({
                 "from":       caller_id,
                 "to":         target_id,

package/codegraph/report.py

@@ -22,7 +22,7 @@ def _build_report(g: dict) -> str:
     god_nodes  = g.get("god_nodes", [])
     generated  = g.get("generated_at", "")
 
-    node_map = {n["id"]: n for n in nodes}
+    node_map = {n["id"]: n for n in nodes if "id" in n}
 
     lines = [
         "# CodeGraph Report",

package/codegraph/scanner.py

@@ -19,7 +19,7 @@ def walk_files(root: str, extra_ignore: set | None = None) -> Iterator[str]:
     ignore = DEFAULT_IGNORE | (extra_ignore or set())
     for dirpath, dirnames, filenames in os.walk(root):
         # Prune ignored dirs in-place so os.walk doesn't descend
-        dirnames[:] = [d for d in dirnames if d not in ignore and not d.startswith(".")]
+        dirnames[:] = [d for d in dirnames if not _should_ignore(d, ignore)]
         for fname in filenames:
             ext = Path(fname).suffix.lower()
             if fname in SKIP_FILENAMES or ext in SKIP_EXTENSIONS:

package/codegraph/server.py

@@ -192,13 +192,30 @@ async def _build(args: dict) -> dict:
 
     all_nodes: list[dict] = []
 
-    for nodes in cached.values():
-        all_nodes.extend(nodes)
+    for rel_path, nodes in cached.items():
+        if nodes:
+            all_nodes.extend(nodes)
+        else:
+            # Previously cached as empty — still add a file-level node so it's visible
+            all_nodes.append({
+                "id":   f"{rel_path}::file::{Path(rel_path).name}",
+                "name": Path(rel_path).name,
+                "type": "file",
+                "file": rel_path,
+            })
 
     for rel_path, abs_path in changed.items():
         cat = classify_file(abs_path)
         if cat in ("code", "sql"):
             nodes = ast_extract(abs_path, rel_path)
+            if not nodes:
+                # Extractor found no symbols — still represent the file so it appears in the graph
+                nodes = [{
+                    "id":   f"{rel_path}::file::{Path(rel_path).name}",
+                    "name": Path(rel_path).name,
+                    "type": "file",
+                    "file": rel_path,
+                }]
             set_cached_nodes(cache, rel_path, file_hash(abs_path), nodes)
             all_nodes.extend(nodes)
         elif cat == "config":
@@ -232,7 +249,7 @@ async def _build(args: dict) -> dict:
     generate_report(graph_dict, root)
     save_cache(root, cache)
     try:
-        export_all(graph_dict, root)
+        export_all(graph_dict, str(Path(root) / "codegraph-cache"))
     except Exception:
         pass
 

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "context-mcp-server",
-  "version": "1.1.1",
-  "description": "Persistent AI memory + codebase knowledge graph MCP server. Works across Claude Code, Cursor, Gemini CLI, Codex, Windsurf, VS Code Copilot, Antigravity IDE, Claude.ai, and ChatGPT.",
+  "version": "1.1.3",
+  "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",

package/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "codegraph-mcp"
-version = "1.1.1"
+version = "1.1.3"
 description = "Codebase knowledge graph MCP server — AST extraction, graph queries, community detection"
 readme = "README.md"
 requires-python = ">=3.11"

package/src/cli.js

@@ -5,7 +5,7 @@
  */
 
 import readline from 'node:readline';
-import { readFileSync, writeFileSync, mkdirSync, existsSync, unlinkSync } from 'node:fs';
+import { readFileSync, writeFileSync, mkdirSync, existsSync, unlinkSync, chmodSync } from 'node:fs';
 import { dirname, join } from 'node:path';
 import { homedir } from 'node:os';
 import { fileURLToPath } from 'node:url';
@@ -414,7 +414,6 @@ const _GLOBAL_GITIGNORE_ENTRIES = [
   '.gemini/',
   '.codex/',
   '.windsurf/',
-  '.agents/',
   // Build outputs and session artifacts
   'codegraph-cache/',
   '.mcp.json',
@@ -429,7 +428,6 @@ function _graphForProject(graphs, projectName) {
 
 const _PROJECT_GITIGNORE_ENTRIES = [
   '.claude/', '.cursor/', '.vscode/', '.gemini/', '.codex/',
-  '.agents/',
   'codegraph-cache/', '.mcp.json', 'CLAUDE.md', 'GEMINI.md', 'AGENTS.md',
 ];
 
@@ -498,7 +496,12 @@ function _copyHooks(platform, dotDir, dir, hookFiles) {
   for (const file of hookFiles) {
     const src = join(hooksSrc, file);
     if (existsSync(src)) {
-      _writeFile(join(hooksDest, file), readFileSync(src, 'utf8'), `${dotDir}/hooks/${file}`);
+      const dest = join(hooksDest, file);
+      _writeFile(dest, readFileSync(src, 'utf8'), `${dotDir}/hooks/${file}`);
+      // Make executable on Unix so shells can run it without explicit `node` prefix
+      if (process.platform !== 'win32') {
+        try { chmodSync(dest, 0o755); } catch {}
+      }
     }
   }
 }
@@ -595,6 +598,14 @@ const PLATFORMS = {
       }
       // Slash commands — user-global
       _writeCommands(homedir());
+      // Rules file — project root for project scope, ~/.claude/CLAUDE.md for global
+      const claudeMd = _tpl('claude/CLAUDE.md');
+      if (claudeMd) {
+        const claudeMdPath = scope === 'project'
+          ? join(dir, 'CLAUDE.md')
+          : join(homedir(), '.claude', 'CLAUDE.md');
+        _writeFile(claudeMdPath, claudeMd, scope === 'project' ? 'CLAUDE.md' : '~/.claude/CLAUDE.md');
+      }
       // Hooks — write into the appropriate settings.json scope
       // Project hooks live in .claude/hooks/ and are committed; user hooks in ~/.claude/hooks/
       const hooksBase = scope === 'project' ? dir : homedir();
@@ -610,11 +621,11 @@ const PLATFORMS = {
       _mergeHooksIntoSettings(settingsPath, {
         PreToolUse: [{
           matcher: 'Bash',
-          hooks: [{ type: 'command', command: preHook, timeout: 30, statusMessage: 'Checking shell command' }],
+          hooks: [{ type: 'command', command: `node "${preHook}"`, timeout: 30, statusMessage: 'Checking shell command' }],
         }],
         PostToolUse: [{
           matcher: 'Bash',
-          hooks: [{ type: 'command', command: postHook, timeout: 30, statusMessage: 'Saving failed shell context' }],
+          hooks: [{ type: 'command', command: `node "${postHook}"`, timeout: 30, statusMessage: 'Saving failed shell context' }],
         }],
       }, scope === 'project' ? '.claude/settings.json' : '~/.claude/settings.json');
       // Register MCP server via claude CLI
@@ -724,26 +735,31 @@ const PLATFORMS = {
       );
       settings.hooks.BeforeTool = stripOld(settings.hooks.BeforeTool).concat([{
         matcher: 'run_shell_command',
-        hooks: [{ type: 'command', command: `node ${beforeHook}`, timeout: 30 }],
+        hooks: [{ type: 'command', command: `node "${beforeHook}"`, timeout: 30 }],
       }]);
       settings.hooks.AfterTool = stripOld(settings.hooks.AfterTool).concat([{
         matcher: 'run_shell_command',
-        hooks: [{ type: 'command', command: `node ${afterHook}`, timeout: 30 }],
+        hooks: [{ type: 'command', command: `node "${afterHook}"`, timeout: 30 }],
       }]);
       _writeFile(settingsPath,
         JSON.stringify(settings, null, 2),
         scope === 'project' ? '.gemini/settings.json' : '~/.gemini/settings.json',
       );
-      // Slash commands (.toml) — project-scoped only
-      if (scope === 'project') {
-        const cmdsSrc = join(TPLS, 'gemini', 'commands');
-        const cmdsDest = join(dir, '.gemini', 'commands');
-        for (const file of ['context-resume.toml', 'graph-build.toml', 'save-context.toml']) {
-          const src = join(cmdsSrc, file);
-          if (existsSync(src)) _writeFile(join(cmdsDest, file), readFileSync(src, 'utf8'), `.gemini/commands/${file}`);
-        }
-        const md = _tpl('gemini/GEMINI.md');
-        if (md) _writeFile(join(dir, 'GEMINI.md'), md, 'GEMINI.md');
+      // Slash commands (.toml) — project: .gemini/commands/, global: ~/.gemini/commands/
+      const geminiCmdsDest = join(hooksBase, '.gemini', 'commands');
+      const cmdsSrc = join(TPLS, 'gemini', 'commands');
+      for (const file of ['context-resume.toml', 'graph-build.toml', 'save-context.toml']) {
+        const src = join(cmdsSrc, file);
+        const label = scope === 'project' ? `.gemini/commands/${file}` : `~/.gemini/commands/${file}`;
+        if (existsSync(src)) _writeFile(join(geminiCmdsDest, file), readFileSync(src, 'utf8'), label);
+      }
+      // Rules file — project root for project scope, ~/.gemini/GEMINI.md for global
+      const geminiMd = _tpl('gemini/GEMINI.md');
+      if (geminiMd) {
+        const geminiMdPath = scope === 'project'
+          ? join(dir, 'GEMINI.md')
+          : join(homedir(), '.gemini', 'GEMINI.md');
+        _writeFile(geminiMdPath, geminiMd, scope === 'project' ? 'GEMINI.md' : '~/.gemini/GEMINI.md');
       }
     },
   },
@@ -754,9 +770,13 @@ const PLATFORMS = {
       const includeHooks = scope === 'project';
       if (includeHooks) _copyCodexHooks(dir);
       _writeFile(join(dir, '.codex', 'config.toml'), _codexConfigToml(dir, includeHooks), '.codex/config.toml');
-      if (scope === 'project') {
-        const md = _tpl('codex/AGENTS.md');
-        if (md) _writeFile(join(dir, 'AGENTS.md'), md, 'AGENTS.md');
+      // Rules file — project root for project scope, ~/.codex/AGENTS.md for global
+      const codexMd = _tpl('codex/AGENTS.md');
+      if (codexMd) {
+        const codexMdPath = scope === 'project'
+          ? join(dir, 'AGENTS.md')
+          : join(homedir(), '.codex', 'AGENTS.md');
+        _writeFile(codexMdPath, codexMd, scope === 'project' ? 'AGENTS.md' : '~/.codex/AGENTS.md');
       }
       // Prompts (slash commands) — always user-global; Codex only loads ~/.codex/prompts/
       const promptsSrc = join(TPLS, 'codex', 'prompts');
@@ -812,34 +832,6 @@ const PLATFORMS = {
       }
     },
   },
-  antigravity: {
-    label: 'Antigravity IDE',
-    restartNote: 'Restart your Antigravity session to pick up hooks and rules.',
-    install(dir, scope) {
-      // Antigravity uses stdio-incompatible MCP transport — integrate via ctx CLI + GEMINI.md instead.
-      if (scope === 'project') {
-        // Post-tool hook — saves failed tool calls to context-mcp via ctx CLI
-        _copyHooks('antigravity', '.agents', dir, ['context-mcp-post-tool-use.js']);
-        const hookPath = join(dir, '.agents', 'hooks', 'context-mcp-post-tool-use.js');
-        _mergeJsonFile(join(dir, '.agents', 'hooks.json'), '.agents/hooks.json', obj => {
-          const strip = arr => (arr || []).filter(h => !String(h.command || '').includes('context-mcp-'));
-          obj.hooks = strip(obj.hooks).concat([{
-            event: 'PostToolUse',
-            command: `node "${hookPath}"`,
-          }]);
-        });
-        // Workflows (slash commands) — .agents/workflows/
-        const wfSrc = join(TPLS, 'antigravity', 'workflows');
-        for (const file of ['context-resume.md', 'graph-build.md', 'save-context.md']) {
-          const src = join(wfSrc, file);
-          if (existsSync(src)) _writeFile(join(dir, '.agents', 'workflows', file), readFileSync(src, 'utf8'), `.agents/workflows/${file}`);
-        }
-        // Rules file — Antigravity reads GEMINI.md at project root
-        const md = _tpl('antigravity/GEMINI.md');
-        if (md) _writeFile(join(dir, 'GEMINI.md'), md, 'GEMINI.md');
-      }
-    },
-  },
 };
 
 async function cmdInstall(args) {
@@ -901,7 +893,7 @@ async function cmdInstall(args) {
 
   if (!keys.length) {
     printSection('Install');
-    console.log(`  ${muted('Usage:')}  ctx install ${faint('[--initial] [--claude] [--cursor] [--vscode] [--gemini] [--codex] [--windsurf] [--antigravity] [--all]')}`);
+    console.log(`  ${muted('Usage:')}  ctx install ${faint('[--initial] [--claude] [--cursor] [--vscode] [--gemini] [--codex] [--windsurf] [--all]')}`);
     console.log('');
     console.log(`  ${accent('--initial      ')}  ${faint('Install / update Node.js + Python (codegraph) deps')}`);
     console.log('');

package/src/db.js

@@ -178,6 +178,11 @@ function findEntryById(id, projectHint) {
     const e = search(data);
     if (e) return { entry: e, projectName: name };
   }
+  // Always check 'global' — it is never in the projects index
+  if (!_projectData.has('global') && 'global' !== projectHint) {
+    const e = search(loadProjectData('global'));
+    if (e) return { entry: e, projectName: 'global' };
+  }
   const idx = loadProjectsIndex();
   for (const proj of idx) {
     if (_projectData.has(proj.name) || proj.name === projectHint) continue;
@@ -384,10 +389,12 @@ export function getContext({ project, tags, limit = 20, compact = false, ids } =
 
   if (ids && ids.length) {
     const idSet = new Set(ids);
-    // Load all projects to find entries
+    // Load all projects to find entries — always include 'global' since it is
+    // never registered in the projects index (ensureProject skips it)
     const idx = loadProjectsIndex();
     const all = [];
     const loaded = new Set(_projectData.keys());
+    loaded.add('global'); // ensure global is always searched
     for (const proj of idx) loaded.add(proj.name);
     for (const name of loaded) {
       for (const e of getAllEntries(name)) {
@@ -403,10 +410,11 @@ export function getContext({ project, tags, limit = 20, compact = false, ids } =
     const globalEntries = project !== 'global' ? getAllEntries('global') : [];
     results = [...entries, ...globalEntries];
   } else {
-    // No project filter: load all
+    // No project filter: load all — always include 'global' since it is never in the index
     const idx = loadProjectsIndex();
     const all = [];
     const seen = new Set(_projectData.keys());
+    seen.add('global');
     for (const proj of idx) seen.add(proj.name);
     for (const name of seen) {
       all.push(...getAllEntries(name));
@@ -434,7 +442,7 @@ export function getContextSince(since, project) {
   } else {
     const idx = loadProjectsIndex();
     results = [];
-    const seen = new Set([..._projectData.keys(), ...idx.map(p => p.name)]);
+    const seen = new Set([..._projectData.keys(), 'global', ...idx.map(p => p.name)]);
     for (const name of seen) results.push(...getAllEntries(name));
   }
   return results.filter(c => c.createdAt >= since);
@@ -450,7 +458,7 @@ export function searchContext({ query, project, limit = 10, compact = false }) {
   } else {
     const idx = loadProjectsIndex();
     results = [];
-    const seen = new Set([..._projectData.keys(), ...idx.map(p => p.name)]);
+    const seen = new Set([..._projectData.keys(), 'global', ...idx.map(p => p.name)]);
     for (const name of seen) results.push(...getAllEntries(name));
   }
   const scored = results.map(c => {
@@ -467,8 +475,9 @@ export function deleteContext({ id, ids }) {
   const idSet = new Set(ids && ids.length ? ids : (id ? [id] : []));
   if (!idSet.size) return { deleted: 0 };
   let deleted = 0;
-  // Scan all loaded projects
+  // Scan all loaded projects — always include 'global' since it is never in the index
   const seen = new Set(_projectData.keys());
+  seen.add('global');
   loadProjectsIndex().forEach(p => seen.add(p.name));
   for (const name of seen) {
     const data = loadProjectData(name);
@@ -524,7 +533,7 @@ export function countContext(project) {
   if (!project) {
     const idx = loadProjectsIndex();
     let total = 0;
-    const seen = new Set([..._projectData.keys(), ...idx.map(p => p.name)]);
+    const seen = new Set([..._projectData.keys(), 'global', ...idx.map(p => p.name)]);
     for (const name of seen) total += getAllEntries(name).length;
     return total;
   }
@@ -658,7 +667,7 @@ export function updateDiscussion({ id, name, title, description, content, status
   let disc = null;
   let projName = null;
   const idx = loadProjectsIndex();
-  const seen = new Set([..._projectData.keys(), ...idx.map(p => p.name)]);
+  const seen = new Set([..._projectData.keys(), 'global', ...idx.map(p => p.name)]);
   for (const pName of seen) {
     const d = loadProjectData(pName);
     const found = id ? d.discussions.find(x => x.id === id) : d.discussions.find(x => x.name === name);
@@ -690,9 +699,9 @@ export function getDiscussion({ project, name, id } = {}) {
     if (name) return list.find(d => d.name === name) || null;
     return null;
   }
-  // Search all
+  // Search all — always include 'global' since it is never in the projects index
   const idx = loadProjectsIndex();
-  const seen = new Set([..._projectData.keys(), ...idx.map(p => p.name)]);
+  const seen = new Set([..._projectData.keys(), 'global', ...idx.map(p => p.name)]);
   for (const pName of seen) {
     const d = loadProjectData(pName);
     const found = id ? d.discussions.find(x => x.id === id) : d.discussions.find(x => x.name === name);
@@ -709,7 +718,7 @@ export function listDiscussions({ project, status, type } = {}) {
     if (project !== 'global') list = [...list, ...loadProjectData('global').discussions];
   } else {
     const idx = loadProjectsIndex();
-    const seen = new Set([..._projectData.keys(), ...idx.map(p => p.name)]);
+    const seen = new Set([..._projectData.keys(), 'global', ...idx.map(p => p.name)]);
     for (const pName of seen) list.push(...loadProjectData(pName).discussions);
   }
   if (status) list = list.filter(d => d.status === status);
@@ -730,7 +739,7 @@ export function linkContextToDiscussion({ discussionId, discussionName, contextI
   let disc = null;
   let discProject = null;
   const idx = loadProjectsIndex();
-  const seen = new Set([..._projectData.keys(), ...idx.map(p => p.name)]);
+  const seen = new Set([..._projectData.keys(), 'global', ...idx.map(p => p.name)]);
   for (const pName of seen) {
     const d = loadProjectData(pName);
     const found = discussionId
@@ -764,7 +773,7 @@ export function linkContextToDiscussion({ discussionId, discussionName, contextI
 export function deleteDiscussion({ name, id }) {
   init();
   const idx = loadProjectsIndex();
-  const seen = new Set([..._projectData.keys(), ...idx.map(p => p.name)]);
+  const seen = new Set([..._projectData.keys(), 'global', ...idx.map(p => p.name)]);
   for (const pName of seen) {
     const data = loadProjectData(pName);
     const before = data.discussions.length;
@@ -803,7 +812,7 @@ export function archiveExpired(project) {
     processEntries(getAllEntries(project), project);
   } else {
     const idx = loadProjectsIndex();
-    const seen = new Set([..._projectData.keys(), ...idx.map(p => p.name)]);
+    const seen = new Set([..._projectData.keys(), 'global', ...idx.map(p => p.name)]);
     for (const name of seen) processEntries(getAllEntries(name).slice(), name);
   }
   if (count > 0) markDirty();

package/src/http.js

@@ -622,7 +622,7 @@ async function handleRequest(req, res) {
               <div class="step">
                 <span class="step-num">2</span>
                 <span class="step-title">Server URL</span>
-                <span class="step-content">Enter: <code>${req.headers['x-forwarded-proto'] || req.socket?.encrypted ? 'https' : 'http'}://${req.headers.host}</code></span>
+                <span class="step-content">Enter: <code>${req.headers['x-forwarded-proto'] === 'https' || req.socket?.encrypted ? 'https' : 'http'}://${req.headers.host}</code></span>
               </div>
 
               <div class="step">

package/src/tools/errorCheck.js

@@ -35,7 +35,7 @@ export async function handle(args, state) {
 
   if (action === 'check') {
     const results = unifiedSearch({ mode: 'semantic', query: errorMessage, project, limit: 5 })
-      .filter(r => r.type === 'bug');
+      .filter(r => Array.isArray(r.tags) && r.tags.includes('error-log'));
     if (results.length > 0 && results[0].similarity > 0.4) {
       return {
         success: true, found: true,
@@ -53,8 +53,8 @@ export async function handle(args, state) {
       sessionId: state.sessionId || null,
       title:   `Error: ${errorMessage.split('\n')[0].slice(0, 60)}`,
       content: `Command: ${command || 'unknown'}\n\nError:\n${errorMessage}\n\nSolution:\n${solution}`,
-      type:    'bug',
-      status:  'done',
+      type:    'note',
+      status:  'active',
       tags:    ['error-log', command].filter(Boolean),
     });
     fireAutoLink(entry.id, state);

package/src/tools/fileTools.js

@@ -107,7 +107,7 @@ export async function handle(name, args, state) {
       saveAutoContext({
         title:   `wrote ${filePath.split(/[\\/]/).pop()}`,
         content: `write_file: created/overwrote ${filePath}`,
-        type:    'code',
+        type:    'note',
         files:   [{ path: filePath, action: 'modified' }],
         tags:    ['file-write'],
         state,
@@ -159,7 +159,7 @@ export async function handle(name, args, state) {
         title:   `patched ${filePath.split(/[\\/]/).pop()}${sorted.length > 1 ? ` (${sorted.length} edits)` : ''}`,
         content: `patch_file: ${sorted.length} edit(s) in ${filePath}\n` +
                  sorted.map(e => `  ${e.description}: -${e.old_str.split('\n').length} +${e.new_str.split('\n').length} lines`).join('\n'),
-        type:    'code',
+        type:    'note',
         files:   [{ path: filePath, action: 'modified' }],
         tags:    ['file-patch'],
         state,

package/src/tools/gitTools.js

@@ -175,7 +175,7 @@ export async function handle(name, args, state) {
       saveAutoContext({
         title:   `git commit: ${args.message.slice(0, 57)}${args.message.length > 57 ? '...' : ''}`,
         content: `hash: ${hash} | branch: ${branch}\nmessage: ${args.message}\nfiles: ${stagedFiles.map(f => f.path).join(', ')}`,
-        type:    'decision',
+        type:    'note',
         files:   stagedFiles,
         tags:    ['git', 'commit', branch],
         state,

package/uv.lock

@@ -201,7 +201,7 @@ wheels = [
 
 [[package]]
 name = "codegraph-mcp"
-version = "1.1.0"
+version = "1.1.2"
 source = { editable = "." }
 dependencies = [
     { name = "mcp" },
@@ -2308,8 +2308,8 @@ name = "uvicorn"
 version = "0.46.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
-    { name = "click" },
-    { name = "h11" },
+    { name = "click", marker = "python_full_version < '3.15' or sys_platform != 'emscripten'" },
+    { name = "h11", marker = "python_full_version < '3.15' or sys_platform != 'emscripten'" },
 ]
 sdist = { url = "https://files.pythonhosted.org/packages/1f/93/041fca8274050e40e6791f267d82e0e2e27dd165627bd640d3e0e378d877/uvicorn-0.46.0.tar.gz", hash = "sha256:fb9da0926999cc6cb22dc7cd71a94a632f078e6ae47ff683c5c420750fb7413d", size = 88758, upload-time = "2026-04-23T07:16:00.151Z" }
 wheels = [