memtrace 0.3.87 → 0.3.90

package/README.md

@@ -61,7 +61,7 @@ All four systems run on the same machine, same mempalace checkout, same 1,000 qu
 
 | Tool | Coverage | Acc@1 | Acc@5 | Acc@10 | Avg lat | Tokens |
 |:-----|---------:|------:|------:|-------:|--------:|-------:|
-| **Memtrace** (ArcadeDB) | **100.0%** | **96.7%** | **100.0%** | **100.0%** | **9.16 ms** | 195 |
+| **Memtrace** (MemDB) | **100.0%** | **96.7%** | **100.0%** | **100.0%** | **9.16 ms** | 195 |
 | ChromaDB (all-MiniLM-L6-v2)     | 100.0%  | 62.3% | 86.1% | 87.9%  |  58.5 ms |  1,937 |
 | GitNexus (eval-server)          |  99.5%  | 27.1% | 89.7% | 89.9%  | 191.2 ms |    213 |
 | CodeGrapherContext (CLI)        |  67.2%  |  6.4% | 66.4% | 66.7%  | 1627.2 ms |    221 |
@@ -117,7 +117,7 @@ GitNexus and CodeGrapherContext both build AST-based code graphs with structural
 
 All numbers from [the fair benchmark](https://github.com/syncable-dev/memtrace-public/tree/main/benchmarks/fair) on the same machine, same mempalace checkout, same 1,000 queries. Ground truth is extracted by Python's stdlib `ast` — not from any tool's index — so no system is advantaged in the dataset itself.
 
-The latency difference is primarily Rust vs. interpreted runtimes, and ArcadeDB's Graph-OLAP engine (native CSR projections, PageRank/betweenness as in-database procedures) vs. HTTP/embedding pipelines. The feature difference is temporal memory and API topology — dimensions Memtrace adds on top of the shared AST-graph foundation.
+The latency difference is primarily Rust vs. interpreted runtimes, and MemDB's embedded native graph engine (in-process Node/Edge storage, bi-temporal predicates resolved at the storage layer, vector + lexical indexes co-located) vs. HTTP/embedding pipelines. The feature difference is temporal memory and API topology — dimensions Memtrace adds on top of the shared AST-graph foundation.
 
 </details>
 
@@ -248,7 +248,7 @@ For manual setup:
 ```bash
 claude plugin marketplace add https://github.com/syncable-dev/memtrace-public.git
 claude plugin install memtrace-skills@memtrace --scope user
-claude mcp add memtrace -- memtrace mcp -e MEMTRACE_ARCADEDB_BOLT_URL=bolt://localhost:7687
+claude mcp add memtrace -- memtrace mcp
 ```
 
 ### Cursor
@@ -299,8 +299,7 @@ For Cline, Roo Code, or any client that only needs MCP tools, add this server ma
   "mcpServers": {
     "memtrace": {
       "command": "memtrace",
-      "args": ["mcp"],
-      "env": { "MEMTRACE_ARCADEDB_BOLT_URL": "bolt://localhost:7687" }
+      "args": ["mcp"]
     }
   }
 }

package/bin/memtrace.js

@@ -262,7 +262,7 @@ async function maybePromptForUpgrade(command) {
     ["install", "-g", "memtrace@latest"],
     spawnOptionsForPlatform(process.platform, {
       stdio: "inherit",
-      env: process.env,
+      env: { ...process.env, MEMTRACE_INSTALL_PARENT: "1" },
     }),
   );
   if (installResult.status !== 0) {

package/installer/dist/transformers/claude.js

@@ -3,6 +3,7 @@ import path from 'path';
 import os from 'os';
 import { execCommand, commandExists } from '../utils.js';
 import { safeReadJson, writeJsonAtomic } from '../fs-safe.js';
+import { MEMTRACE_MCP_ENV } from './shared.js';
 const PLUGIN_NAME = 'memtrace-skills';
 const MARKETPLACE_NAME = 'memtrace';
 const MARKETPLACE_REPO = 'syncable-dev/memtrace-public';
@@ -33,7 +34,7 @@ async function tryMcpAddJson(memtraceBinary) {
     const config = JSON.stringify({
         command: memtraceBinary,
         args: ['mcp'],
-        env: { MEMTRACE_ARCADEDB_BOLT_URL: 'bolt://localhost:7687' },
+        env: MEMTRACE_MCP_ENV,
     });
     // Shell-quote the JSON. Use single quotes; escape any embedded single quote.
     const escaped = config.replace(/'/g, `'\\''`);
@@ -166,7 +167,7 @@ export function registerMcpInSettingsAt(settingsPath, memtraceBinary) {
     settings.mcpServers['memtrace'] = {
         command: memtraceBinary,
         args: ['mcp'],
-        env: { MEMTRACE_ARCADEDB_BOLT_URL: 'bolt://localhost:7687' },
+        env: MEMTRACE_MCP_ENV,
     };
     writeJsonAtomic(settingsPath, settings);
     return { registered: true };
@@ -418,7 +419,7 @@ function writeClaudeLocalMcp(mcpPath, binary) {
     cfg.mcpServers['memtrace'] = {
         command: binary,
         args: ['mcp'],
-        env: { MEMTRACE_ARCADEDB_BOLT_URL: 'bolt://localhost:7687' },
+        env: MEMTRACE_MCP_ENV,
     };
     writeJsonAtomic(mcpPath, cfg);
     return true;

package/installer/dist/transformers/cursor.js

@@ -2,6 +2,7 @@ import fs from 'fs';
 import os from 'os';
 import path from 'path';
 import { safeReadJson, writeJsonAtomic } from '../fs-safe.js';
+import { MEMTRACE_MCP_ENV } from './shared.js';
 function skillsRoot(ctx) {
     const base = ctx.scope === 'global' ? os.homedir() : ctx.cwd;
     return path.join(base, '.cursor', 'skills');
@@ -30,7 +31,7 @@ export function registerCursorMcpAt(mcpFile, binary) {
     cfg.mcpServers['memtrace'] = {
         command: binary,
         args: ['mcp'],
-        env: { MEMTRACE_ARCADEDB_BOLT_URL: 'bolt://localhost:7687' },
+        env: MEMTRACE_MCP_ENV,
     };
     writeJsonAtomic(mcpFile, cfg);
     return { registered: true };

package/installer/dist/transformers/shared.d.ts

@@ -1,8 +1,6 @@
 import { Skill } from '../skills.js';
 export declare const MCP_SERVER_NAME = "memtrace";
-export declare const MEMTRACE_MCP_ENV: {
-    MEMTRACE_ARCADEDB_BOLT_URL: string;
-};
+export declare const MEMTRACE_MCP_ENV: Record<string, string>;
 export declare function skillName(skill: Skill): string;
 export declare function skillMarkdown(skill: Skill, extraFrontmatter?: Record<string, string>): string;
 export declare function writeSkills(skills: Skill[], rootDir: string, extraFrontmatter?: Record<string, string>): number;

package/installer/dist/transformers/shared.js

@@ -2,7 +2,13 @@ import fs from 'fs';
 import path from 'path';
 import { safeReadJson, writeJsonAtomic } from '../fs-safe.js';
 export const MCP_SERVER_NAME = 'memtrace';
-export const MEMTRACE_MCP_ENV = { MEMTRACE_ARCADEDB_BOLT_URL: 'bolt://localhost:7687' };
+// Phase 3 (ArcadeDB removal): the binary uses an embedded MemDB by default and
+// reads MEMTRACE_MEMDB_MODE / workspace anchors directly. No env vars are
+// required at MCP-registration time. Preserved as an empty constant so any
+// future env-var plumbing (e.g. RUST_LOG, MEMTRACE_DATA_DIR overrides) has
+// one place to land. The corresponding upgrade migration in install.js strips
+// any legacy MEMTRACE_ARCADEDB_* keys from existing MCP entries on upgrade.
+export const MEMTRACE_MCP_ENV = {};
 export function skillName(skill) {
     return skill.filename.replace(/\.md$/, '');
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "memtrace",
-  "version": "0.3.87",
+  "version": "0.3.90",
   "description": "Code intelligence graph — MCP server + AI agent skills + visualization UI",
   "keywords": [
     "mcp",
@@ -39,11 +39,11 @@
     "fs-extra": "^11.0.0"
   },
   "optionalDependencies": {
-    "@memtrace/darwin-arm64": "0.3.87",
-    "@memtrace/linux-x64": "0.3.87",
-    "@memtrace/win32-x64": "0.3.87",
-    "@memtrace/linux-x64-noavx2": "0.3.87",
-    "@memtrace/win32-x64-noavx2": "0.3.87"
+    "@memtrace/darwin-arm64": "0.3.90",
+    "@memtrace/linux-x64": "0.3.90",
+    "@memtrace/win32-x64": "0.3.90",
+    "@memtrace/linux-x64-noavx2": "0.3.90",
+    "@memtrace/win32-x64-noavx2": "0.3.90"
   },
   "engines": {
     "node": ">=18"

package/uninstall.js

@@ -223,6 +223,28 @@ function removeMemtraceHomeDir(home = os.homedir()) {
   }
 }
 
+function isUpgradeLifecycle(env = process.env) {
+  if (env.MEMTRACE_INSTALL_PARENT === "1") {
+    return true;
+  }
+
+  // npm can run an installed package's preuninstall lifecycle while replacing
+  // it during `npm install -g memtrace@latest`. That is an upgrade, not a user
+  // data purge. Explicit `npm uninstall -g memtrace` reports npm_command as
+  // "uninstall"; data purge still requires MEMTRACE_PURGE_DATA=1.
+  if (env.npm_lifecycle_event !== "preuninstall") {
+    return false;
+  }
+  return ["install", "update", "upgrade"].includes(env.npm_command);
+}
+
+function shouldPurgeMemtraceHomeDir(env = process.env) {
+  if (isUpgradeLifecycle(env)) {
+    return false;
+  }
+  return env.MEMTRACE_PURGE_DATA === "1" || env.MEMTRACE_UNINSTALL_PURGE_DATA === "1";
+}
+
 // ── Try Claude CLI uninstall ────────────────────────────────────────────────
 
 function tryClaudeCliUninstall() {
@@ -272,7 +294,85 @@ function legacyCleanup(options = {}) {
   removeClaudeIntegration(home);
 }
 
+function killRunningMemtraceProcesses(env = process.env) {
+  // npm's atomic global install on macOS / Linux works by renaming the
+  // existing `node_modules/memtrace` directory aside (to a `.memtrace-XXXX`
+  // tempname) before extracting the new tarball. If any memtrace process
+  // is still running — a long-lived daemon from `memtrace start`, an MCP
+  // server an agent left attached, the file watcher — the binary on disk
+  // is mmap'd into that process and the rename fails with ENOTEMPTY,
+  // leaving both the old dir AND a partially-renamed temp dir on disk.
+  // The user then has to manually rm both and retry. We can prevent that
+  // by killing memtrace processes BEFORE npm tries the rename — which is
+  // exactly what the preuninstall hook (this script) runs.
+  //
+  // Self-upgrade case: `memtrace install` sets MEMTRACE_INSTALL_PARENT=1
+  // before spawning npm, so the running memtrace binary is OUR PARENT.
+  // Killing it would abort the npm install we're a child of. Skip in
+  // that path — the parent will exit cleanly after its npm child returns
+  // and the rename will succeed on its way out.
+  if (env.MEMTRACE_INSTALL_PARENT === "1") {
+    return;
+  }
+
+  const tryKill = (cmd, args) => {
+    try {
+      spawnSync(cmd, args, { stdio: "ignore" });
+    } catch {
+      // taskkill / pkill missing from PATH is rare but possible inside
+      // pared-down containers or locked-down enterprise images. We don't
+      // want to abort the user's install because a process-killer isn't
+      // installed — fall through and let npm's rename try its luck.
+    }
+  };
+
+  if (process.platform === "win32") {
+    // /F  = force terminate
+    // /T  = also kill child processes (file watchers, embed-worker children
+    //       spawned by `memtrace start`, MCP server's notify-rs threads)
+    // /IM = match by image name; covers every launcher because the npm
+    //       shim execs the same `memtrace.exe` binary regardless of
+    //       `start` / `mcp` / `daemon` argv.
+    tryKill("taskkill", ["/F", "/T", "/IM", "memtrace.exe"]);
+    // Defensive: some Windows installs end up with a `node.exe` running
+    // `memtrace.js` (the npm shim) that hasn't yet exec'd the platform
+    // binary. Kill any node process whose command line references our
+    // shim path via PowerShell — wrapped so a missing PS install (rare
+    // on modern Windows but possible on Server Core) doesn't abort.
+    tryKill("powershell", [
+      "-NoProfile",
+      "-NonInteractive",
+      "-Command",
+      "Get-CimInstance Win32_Process -Filter \"Name='node.exe'\" | " +
+        "Where-Object { $_.CommandLine -like '*memtrace*\\bin\\memtrace.js*' } | " +
+        "ForEach-Object { Stop-Process -Id $_.ProcessId -Force -ErrorAction SilentlyContinue }",
+    ]);
+  } else {
+    // Three patterns cover every launcher shape the binary exposes.
+    // `pkill -f` matches against the full command line, so `memtrace mcp`
+    // catches both the npm-shim invocation AND the platform binary it
+    // exec'd into. Missing-process exit (1) is ignored via stdio: ignore.
+    tryKill("pkill", ["-9", "-f", "memtrace mcp"]);
+    tryKill("pkill", ["-9", "-f", "memtrace start"]);
+    tryKill("pkill", ["-9", "-f", "memtrace daemon"]);
+  }
+
+  // Settle window: SIGKILL / taskkill is synchronous but the OS needs a
+  // tick to tear down mmap'd page tables and release directory entries.
+  // - macOS / Linux: 200ms is enough on every machine tested; the vnode
+  //   reference usually drops within ~50ms after TASK_INACTIVE.
+  // - Windows: longer hold because Windows Defender, Search Indexer, and
+  //   any OneDrive sync agent each take a file-handle reference when the
+  //   binary exits. 750ms is empirically enough to clear those — well
+  //   under any human-noticeable install delay.
+  const settleMs = process.platform === "win32" ? 750 : 200;
+  const until = Date.now() + settleMs;
+  // eslint-disable-next-line no-empty
+  while (Date.now() < until) {}
+}
+
 function run() {
+  killRunningMemtraceProcesses();
   console.log("memtrace: cleaning up...");
 
   // Try delegating to the compiled installer (handles ALL agents via registry)
@@ -293,9 +393,12 @@ function run() {
     legacyCleanup();
   }
 
-  // Always clean up ~/.memtrace/
-  if (removeMemtraceHomeDir()) {
+  if (isUpgradeLifecycle()) {
+    console.log("memtrace: preserving ~/.memtrace/ during upgrade");
+  } else if (shouldPurgeMemtraceHomeDir() && removeMemtraceHomeDir()) {
     console.log("memtrace: removed ~/.memtrace/");
+  } else {
+    console.log("memtrace: preserving ~/.memtrace/ user data");
   }
 
   console.log("memtrace: uninstall complete");
@@ -319,6 +422,9 @@ module.exports = {
   removeMarketplaceCaches,
   removeInstalledPluginMetadata,
   removeMemtraceHomeDir,
+  isUpgradeLifecycle,
+  shouldPurgeMemtraceHomeDir,
+  killRunningMemtraceProcesses,
   removeClaudeIntegration,
   legacyCleanup,
 };