@neat.is/core 0.4.16 → 0.4.18

package/dist/cli.js

@@ -1,4 +1,7 @@
 #!/usr/bin/env node
+import {
+  readDaemonRecord
+} from "./chunk-GXWBMJDJ.js";
 import {
   buildSearchIndex
 } from "./chunk-XOOCA5T7.js";
@@ -24,10 +27,12 @@ import {
   ensureCompatLoaded,
   evaluateAllPolicies,
   extractFromDirectory,
+  findDaemonByProject,
   formatExtractionBanner,
   formatPrecisionFloorBanner,
   getGraph,
   isStrictExtractionEnabled,
+  listMachineProjects,
   listProjects,
   loadGraphFromDisk,
   loadPolicyFile,
@@ -36,25 +41,28 @@ import {
   normalizeProjectPath,
   pathsForProject,
   promoteFrontierNodes,
+  pruneRegistry,
+  removeDaemonRecord,
   removeProject,
   resetGraph,
   retireEdgesByFile,
   runPackageManagerInstall,
   saveGraphToDisk,
   setStatus,
+  signalDaemonStop,
   startPersistLoop,
   startStalenessLoop
-} from "./chunk-XS4CGNRO.js";
+} from "./chunk-T3X6XJPU.js";
 import {
   startOtelGrpcReceiver
-} from "./chunk-GHPHVXYM.js";
+} from "./chunk-MTXF77TN.js";
 import {
   __dirname,
   __require,
   assertBindAuthority,
   buildOtelReceiver,
   readAuthEnv
-} from "./chunk-6CO7C4IU.js";
+} from "./chunk-BGPWBRLU.js";
 
 // src/cli.ts
 import path9 from "path";
@@ -744,9 +752,50 @@ import semver from "semver";
 
 // src/installers/templates.ts
 var OTEL_INIT_HEADER = "// Generated by `neat init --apply` (ADR-069). OpenTelemetry auto-instrumentation hook.";
-var OTEL_INIT_STAMP = "// neat-template-version: 5 \u2014 layered file-first capture (ADR-090) + http/json protocol pin (#468).";
+var OTEL_INIT_STAMP = "// neat-template-version: 6 \u2014 daemon.json endpoint resolution (ADR-096) + layered file-first capture (ADR-090).";
 var OTEL_OTLP_HEADERS_JS = "if (process.env.NEAT_OTEL_TOKEN) process.env.OTEL_EXPORTER_OTLP_HEADERS ||= 'Authorization=Bearer ' + process.env.NEAT_OTEL_TOKEN";
 var OTEL_OTLP_PROTOCOL_JS = "process.env.OTEL_EXPORTER_OTLP_PROTOCOL ||= 'http/json'";
+var OTEL_ENDPOINT_RESOLVER_CJS = `;(function () {
+  try {
+    if (process.env.OTEL_EXPORTER_OTLP_TRACES_ENDPOINT || process.env.OTEL_EXPORTER_OTLP_ENDPOINT) return
+    const __neatFs = require('node:fs')
+    const __neatPath = require('node:path')
+    let __neatDir = process.cwd()
+    for (let __i = 0; __i < 8; __i++) {
+      try {
+        const __rec = JSON.parse(__neatFs.readFileSync(__neatPath.join(__neatDir, 'neat-out', 'daemon.json'), 'utf8'))
+        if (__rec && __rec.ports && typeof __rec.ports.otlp === 'number') {
+          process.env.OTEL_EXPORTER_OTLP_TRACES_ENDPOINT = 'http://localhost:' + __rec.ports.otlp + '/v1/traces'
+          break
+        }
+      } catch (_e) {}
+      const __parent = __neatPath.dirname(__neatDir)
+      if (__parent === __neatDir) break
+      __neatDir = __parent
+    }
+  } catch (_e) {}
+  process.env.OTEL_EXPORTER_OTLP_TRACES_ENDPOINT ||= 'http://localhost:4318/v1/traces'
+})()`;
+var OTEL_ESM_NODE_IMPORTS = "import { readFileSync as __neatReadFileSync } from 'node:fs'\nimport { join as __neatJoin, dirname as __neatDirname } from 'node:path'";
+var OTEL_ENDPOINT_RESOLVER_ESM = `;(function () {
+  try {
+    if (process.env.OTEL_EXPORTER_OTLP_TRACES_ENDPOINT || process.env.OTEL_EXPORTER_OTLP_ENDPOINT) return
+    let __neatDir = process.cwd()
+    for (let __i = 0; __i < 8; __i++) {
+      try {
+        const __rec = JSON.parse(__neatReadFileSync(__neatJoin(__neatDir, 'neat-out', 'daemon.json'), 'utf8'))
+        if (__rec && __rec.ports && typeof __rec.ports.otlp === 'number') {
+          process.env.OTEL_EXPORTER_OTLP_TRACES_ENDPOINT = 'http://localhost:' + __rec.ports.otlp + '/v1/traces'
+          break
+        }
+      } catch (_e) {}
+      const __parent = __neatDirname(__neatDir)
+      if (__parent === __neatDir) break
+      __neatDir = __parent
+    }
+  } catch (_e) {}
+  process.env.OTEL_EXPORTER_OTLP_TRACES_ENDPOINT ||= 'http://localhost:4318/v1/traces'
+})()`;
 function neatCaptureSource(ts) {
   const spanT = ts ? ": any" : "";
   const strOpt = ts ? ": string | undefined" : "";
@@ -1035,7 +1084,7 @@ try {
 var OTEL_INIT_CJS = `${OTEL_INIT_HEADER}
 ${OTEL_INIT_STAMP}
 process.env.OTEL_SERVICE_NAME ||= '__SERVICE_NAME__'
-process.env.OTEL_EXPORTER_OTLP_TRACES_ENDPOINT ||= 'http://localhost:4318/projects/__PROJECT__/v1/traces'
+${OTEL_ENDPOINT_RESOLVER_CJS}
 ${OTEL_OTLP_PROTOCOL_JS}
 ${OTEL_OTLP_HEADERS_JS}
 
@@ -1053,8 +1102,9 @@ ${neatWireCaptureSource(false)}
 `;
 var OTEL_INIT_ESM = `${OTEL_INIT_HEADER}
 ${OTEL_INIT_STAMP}
+${OTEL_ESM_NODE_IMPORTS}
 process.env.OTEL_SERVICE_NAME ||= '__SERVICE_NAME__'
-process.env.OTEL_EXPORTER_OTLP_TRACES_ENDPOINT ||= 'http://localhost:4318/projects/__PROJECT__/v1/traces'
+${OTEL_ENDPOINT_RESOLVER_ESM}
 ${OTEL_OTLP_PROTOCOL_JS}
 ${OTEL_OTLP_HEADERS_JS}
 
@@ -1077,8 +1127,9 @@ ${OTEL_INIT_STAMP}
 // strict user tsconfig would reject; suppressing type-checking here keeps the
 // generated file from breaking the host project's \`tsc\` gate (#427) without
 // constraining the runtime logic. The file is regenerated, never hand-edited.
+${OTEL_ESM_NODE_IMPORTS}
 process.env.OTEL_SERVICE_NAME ||= '__SERVICE_NAME__'
-process.env.OTEL_EXPORTER_OTLP_TRACES_ENDPOINT ||= 'http://localhost:4318/projects/__PROJECT__/v1/traces'
+${OTEL_ENDPOINT_RESOLVER_ESM}
 ${OTEL_OTLP_PROTOCOL_JS}
 ${OTEL_OTLP_HEADERS_JS}
 
@@ -1100,11 +1151,14 @@ ${registrations.join("\n")}
 `;
   return template.replace(/__SERVICE_NAME__/g, serviceName).replace(/__PROJECT__/g, projectName).replace(/__INSTRUMENTATION_BLOCK__\n?/g, block);
 }
-function renderEnvNeat(serviceName, projectName) {
+function renderEnvNeat(serviceName, _projectName) {
   return [
     "# Generated by `neat init --apply` (ADR-069).",
     `OTEL_SERVICE_NAME=${serviceName}`,
-    `OTEL_EXPORTER_OTLP_TRACES_ENDPOINT=http://localhost:4318/projects/${projectName}/v1/traces`,
+    "# Advisory only \u2014 the generated otel-init resolves the live endpoint from",
+    "# <project>/neat-out/daemon.json (ports.otlp) at boot (ADR-096). This is the",
+    "# canonical default the daemon takes when its first-choice OTLP port is free.",
+    "OTEL_EXPORTER_OTLP_TRACES_ENDPOINT=http://localhost:4318/v1/traces",
     "OTEL_EXPORTER_OTLP_PROTOCOL=http/json",
     "# Set NEAT_OTEL_TOKEN to the daemon's OTLP secret to authenticate exported spans (#410).",
     "# NEAT_OTEL_TOKEN=",
@@ -1127,8 +1181,9 @@ export async function register() {
 }
 `;
 var NEXT_INSTRUMENTATION_NODE_TS = `${NEXT_INSTRUMENTATION_HEADER}
+${OTEL_ESM_NODE_IMPORTS}
 process.env.OTEL_SERVICE_NAME ||= '__SERVICE_NAME__'
-process.env.OTEL_EXPORTER_OTLP_TRACES_ENDPOINT ||= 'http://localhost:4318/projects/__PROJECT__/v1/traces'
+${OTEL_ENDPOINT_RESOLVER_ESM}
 ${OTEL_OTLP_PROTOCOL_JS}
 ${OTEL_OTLP_HEADERS_JS}
 
@@ -1141,7 +1196,7 @@ new NodeSDK({ instrumentations }).start()
 `;
 var NEXT_INSTRUMENTATION_NODE_JS = `${NEXT_INSTRUMENTATION_HEADER}
 process.env.OTEL_SERVICE_NAME ||= '__SERVICE_NAME__'
-process.env.OTEL_EXPORTER_OTLP_TRACES_ENDPOINT ||= 'http://localhost:4318/projects/__PROJECT__/v1/traces'
+${OTEL_ENDPOINT_RESOLVER_CJS}
 ${OTEL_OTLP_PROTOCOL_JS}
 ${OTEL_OTLP_HEADERS_JS}
 
@@ -1160,8 +1215,9 @@ ${registrations.join("\n")}
 }
 var FRAMEWORK_OTEL_INIT_HEADER = "// Generated by `neat init --apply` (ADR-074). OpenTelemetry SDK hook.";
 var FRAMEWORK_OTEL_INIT_TS_BODY = `${FRAMEWORK_OTEL_INIT_HEADER}
+${OTEL_ESM_NODE_IMPORTS}
 process.env.OTEL_SERVICE_NAME ||= '__SERVICE_NAME__'
-process.env.OTEL_EXPORTER_OTLP_TRACES_ENDPOINT ||= 'http://localhost:4318/projects/__PROJECT__/v1/traces'
+${OTEL_ENDPOINT_RESOLVER_ESM}
 ${OTEL_OTLP_PROTOCOL_JS}
 ${OTEL_OTLP_HEADERS_JS}
 
@@ -1176,7 +1232,7 @@ sdk.start()
 `;
 var FRAMEWORK_OTEL_INIT_JS_BODY = `${FRAMEWORK_OTEL_INIT_HEADER}
 process.env.OTEL_SERVICE_NAME ||= '__SERVICE_NAME__'
-process.env.OTEL_EXPORTER_OTLP_TRACES_ENDPOINT ||= 'http://localhost:4318/projects/__PROJECT__/v1/traces'
+${OTEL_ENDPOINT_RESOLVER_CJS}
 ${OTEL_OTLP_PROTOCOL_JS}
 ${OTEL_OTLP_HEADERS_JS}
 
@@ -2833,10 +2889,6 @@ async function fetchDaemonHealth(restPort) {
     });
   });
 }
-async function checkDaemonHealth(restPort) {
-  const body = await fetchDaemonHealth(restPort);
-  return body !== null;
-}
 async function probeProjectHealth(restPort, name) {
   return new Promise((resolve) => {
     const req = http.get(
@@ -2912,12 +2964,6 @@ async function isPortFree(port) {
     server.listen(port, "127.0.0.1");
   });
 }
-async function probePortsFree() {
-  for (const port of NEAT_PORTS) {
-    if (!await isPortFree(port)) return { free: false, held: port };
-  }
-  return { free: true };
-}
 function formatPortCollisionMessage(port) {
   return [
     `neat: port ${port} is in use; the NEAT daemon needs it.`,
@@ -2925,7 +2971,78 @@ function formatPortCollisionMessage(port) {
     `      \`lsof -i :${port}\` to find the holding process.`
   ];
 }
-function spawnDaemonDetached() {
+var PORT_ALLOCATION_ATTEMPTS = 8;
+var PORT_STRIDE = 1;
+async function tripleFree(ports) {
+  for (const p of [ports.rest, ports.otlp, ports.web]) {
+    if (!await isPortFree(p)) return false;
+  }
+  return true;
+}
+async function allocatePorts() {
+  const [baseRest, baseOtlp, baseWeb] = NEAT_PORTS;
+  for (let i = 0; i < PORT_ALLOCATION_ATTEMPTS; i++) {
+    const candidate = {
+      rest: baseRest + i * PORT_STRIDE,
+      otlp: baseOtlp + i * PORT_STRIDE,
+      web: baseWeb + i * PORT_STRIDE
+    };
+    if (await tripleFree(candidate)) return candidate;
+  }
+  return null;
+}
+async function persistedPortsFor(scanPath) {
+  const record = await readDaemonRecord(scanPath);
+  if (!record) return null;
+  return { rest: record.ports.rest, otlp: record.ports.otlp, web: record.ports.web };
+}
+async function acquireSpawnLock(scanPath) {
+  const lockPath = path7.join(scanPath, "neat-out", "daemon.spawn.lock");
+  await fs6.mkdir(path7.dirname(lockPath), { recursive: true });
+  const STALE_LOCK_MS = 6e4;
+  try {
+    const fd = await fs6.open(lockPath, "wx");
+    await fd.writeFile(`${process.pid}
+`, "utf8");
+    await fd.close();
+    return async () => {
+      await fs6.unlink(lockPath).catch(() => {
+      });
+    };
+  } catch (err) {
+    if (err.code !== "EEXIST") return null;
+    try {
+      const stat = await fs6.stat(lockPath);
+      if (Date.now() - stat.mtimeMs > STALE_LOCK_MS) {
+        await fs6.unlink(lockPath).catch(() => {
+        });
+        return acquireSpawnLock(scanPath);
+      }
+    } catch {
+      return acquireSpawnLock(scanPath);
+    }
+    return null;
+  }
+}
+async function waitForPeerDaemon(restPort, project, timeoutMs) {
+  const deadline = Date.now() + timeoutMs;
+  while (Date.now() < deadline) {
+    if (await healthIsForProject(restPort, project)) return true;
+    await new Promise((r) => setTimeout(r, PROBE_INTERVAL_MS));
+  }
+  return healthIsForProject(restPort, project);
+}
+async function healthIsForProject(restPort, project) {
+  const body = await fetchDaemonHealth(restPort);
+  if (body === null) return false;
+  const named = body.project;
+  if (typeof named === "string") return named === project;
+  if (Array.isArray(body.projects)) {
+    return body.projects.some((p) => p.name === project);
+  }
+  return false;
+}
+function spawnDaemonDetached(spec) {
   const here = path7.dirname(new URL(import.meta.url).pathname);
   const candidates = [
     path7.join(here, "neatd.cjs"),
@@ -2949,6 +3066,13 @@ function spawnDaemonDetached() {
   if (!hasToken && (!env.HOST || env.HOST.length === 0)) {
     env.HOST = "127.0.0.1";
   }
+  if (spec) {
+    env.NEAT_PROJECT = spec.project;
+    env.NEAT_PROJECT_PATH = spec.projectPath;
+    env.PORT = String(spec.ports.rest);
+    env.OTEL_PORT = String(spec.ports.otlp);
+    env.NEAT_WEB_PORT = String(spec.ports.web);
+  }
   const child = spawn2(process.execPath, [entry2, "start"], {
     detached: true,
     // stderr inherits the orchestrator's fd so the daemon's
@@ -3068,48 +3192,75 @@ async function runOrchestrator(opts) {
       result.exitCode = 1;
     }
   }
-  const restPort = Number(process.env.PORT ?? 8080);
   const timeoutMs = opts.daemonReadyTimeoutMs ?? DEFAULT_DAEMON_READY_TIMEOUT_MS;
-  if (await checkDaemonHealth(restPort)) {
+  const persistedPorts = await persistedPortsFor(opts.scanPath);
+  let allocated = null;
+  if (persistedPorts && await healthIsForProject(persistedPorts.rest, currentProjectName)) {
     result.steps.daemon = "already-running";
+    allocated = persistedPorts;
   } else {
-    const probe = await probePortsFree();
-    if (!probe.free) {
-      for (const line of formatPortCollisionMessage(probe.held)) {
+    if (persistedPorts && await isPortFree(persistedPorts.rest) && await tripleFree(persistedPorts)) {
+      allocated = persistedPorts;
+    } else {
+      allocated = await allocatePorts();
+    }
+    if (!allocated) {
+      for (const line of formatPortCollisionMessage(NEAT_PORTS[0])) {
         console.error(line);
       }
       result.exitCode = 3;
       return result;
     }
-    try {
-      spawnDaemonDetached();
-    } catch (err) {
-      console.error(`neat: daemon spawn failed \u2014 ${err.message}`);
-      result.exitCode = 1;
-      return result;
-    }
-    const ready = await waitForDaemonReady(restPort, timeoutMs);
-    result.steps.daemon = ready.ready ? "spawned" : "timed-out";
-    if (!ready.ready) {
-      console.error(`neat: daemon did not become ready within ${timeoutMs}ms`);
-      if (ready.stillBootstrapping.length > 0) {
-        console.error(
-          `neat: still bootstrapping: ${ready.stillBootstrapping.join(", ")}`
-        );
+    const release = await acquireSpawnLock(opts.scanPath);
+    if (!release) {
+      const reused = await waitForPeerDaemon(allocated.rest, currentProjectName, timeoutMs);
+      if (reused) {
+        result.steps.daemon = "already-running";
+      } else {
+        console.error("neat: another `neat` is spawning this project but its daemon did not come up in time");
+        result.exitCode = 1;
+        return result;
       }
-      if (ready.brokenProjects.length > 0) {
-        console.error(`neat: broken projects: ${ready.brokenProjects.join(", ")}`);
+    } else {
+      try {
+        if (await healthIsForProject(allocated.rest, currentProjectName)) {
+          result.steps.daemon = "already-running";
+        } else {
+          spawnDaemonDetached({
+            project: currentProjectName,
+            projectPath: opts.scanPath,
+            ports: allocated
+          });
+          const ready = await waitForDaemonReady(allocated.rest, timeoutMs);
+          result.steps.daemon = ready.ready ? "spawned" : "timed-out";
+          if (!ready.ready) {
+            console.error(`neat: daemon did not become ready within ${timeoutMs}ms`);
+            if (ready.stillBootstrapping.length > 0) {
+              console.error(`neat: still bootstrapping: ${ready.stillBootstrapping.join(", ")}`);
+            }
+            if (ready.brokenProjects.length > 0) {
+              console.error(`neat: broken projects: ${ready.brokenProjects.join(", ")}`);
+            }
+            result.exitCode = 1;
+            return result;
+          }
+          if (ready.brokenProjects.length > 0) {
+            console.warn(
+              `neat: ${ready.brokenProjects.length} project(s) reported broken: ${ready.brokenProjects.join(", ")}`
+            );
+          }
+        }
+      } catch (err) {
+        console.error(`neat: daemon spawn failed \u2014 ${err.message}`);
+        result.exitCode = 1;
+        return result;
+      } finally {
+        await release();
       }
-      result.exitCode = 1;
-      return result;
-    }
-    if (ready.brokenProjects.length > 0) {
-      console.warn(
-        `neat: ${ready.brokenProjects.length} project(s) reported broken: ${ready.brokenProjects.join(", ")}`
-      );
     }
   }
-  const dashboardUrl = opts.dashboardUrl ?? "http://localhost:6328";
+  const webPort = allocated?.web ?? NEAT_PORTS[2];
+  const dashboardUrl = opts.dashboardUrl ?? `http://localhost:${webPort}`;
   if (opts.noOpen || !process.stdout.isTTY) {
     result.steps.browser = "skipped";
   } else {
@@ -3677,7 +3828,7 @@ async function resolveProjectEntry(opts) {
   }
   return null;
 }
-async function checkDaemonHealth2(baseUrl) {
+async function checkDaemonHealth(baseUrl) {
   try {
     const res = await fetch(`${baseUrl.replace(/\/$/, "")}/health`, {
       signal: AbortSignal.timeout(1500)
@@ -3778,7 +3929,7 @@ async function runSync(opts) {
       }
     } else {
       const daemonUrl = opts.daemonUrl ?? process.env.NEAT_API_URL ?? "http://localhost:8080";
-      const healthy = await checkDaemonHealth2(daemonUrl);
+      const healthy = await checkDaemonHealth(daemonUrl);
       if (healthy) {
         try {
           await pushSnapshotToRemote({
@@ -3852,12 +4003,18 @@ function usage() {
   console.log("  watch <path>   Start neat-core, watch <path>, re-extract on changes.");
   console.log("                 PORT (default 8080), OTEL_PORT (4318), HOST (0.0.0.0)");
   console.log("                 control listeners. NEAT_OTLP_GRPC=true also opens 4317.");
-  console.log("  list           List every project registered in the machine-level registry.");
-  console.log("  pause <name>   Mark a project paused \u2014 daemon stops watching until resumed.");
-  console.log("  resume <name>  Mark a project active again.");
+  console.log("  list           Report the daemons running on this machine (alias: ps).");
+  console.log("                 Reads ~/.neat/daemons/ and folds in any registered");
+  console.log("                 project no daemon has self-described yet.");
+  console.log("  ps             Alias of list.");
+  console.log("  pause <name>   Stop a project's daemon until it is started again.");
+  console.log("  resume <name>  Bring a paused project back; for a stopped daemon, re-run");
+  console.log("                 `neat <path>` to start it.");
   console.log("  uninstall <name>");
-  console.log("                 Remove a project from the registry. Does not touch");
+  console.log("                 Stop a project's daemon and retire it. Does not touch");
   console.log("                 neat-out/, policy.json, or any user file.");
+  console.log("  prune          Drop registry entries whose path is gone from disk.");
+  console.log("                 Flags: --json   emit the removed list as JSON");
   console.log("  version        Print the installed @neat.is/core version and exit.");
   console.log("                 Aliases: --version, -v.");
   console.log("  skill          Install or print the Claude Code MCP drop-in.");
@@ -3917,6 +4074,7 @@ function usage() {
   console.log("");
   console.log("environment:");
   console.log("  NEAT_API_URL    base URL for the core REST API (default http://localhost:8080)");
+  console.log("                  alias: NEAT_CORE_URL (the name the MCP server reads)");
   console.log("  NEAT_PROJECT    project name when --project isn't passed");
 }
 var STRING_FLAGS = [
@@ -4050,6 +4208,14 @@ function printVersion() {
   process.stdout.write(`${readPackageVersion()}
 `);
 }
+function formatMachineProjectRow(r) {
+  if (r.ports) {
+    const where = r.pid !== void 0 ? `	pid=${r.pid}` : "";
+    return `${r.project}	${r.state}	rest=${r.ports.rest} otlp=${r.ports.otlp} web=${r.ports.web}	${r.projectPath}${where}`;
+  }
+  const status = r.registryStatus ? `	(${r.registryStatus})` : "";
+  return `${r.project}	${r.state}${status}	${r.projectPath}`;
+}
 function printDiscoveryReport(opts, services) {
   const languages = [...new Set(services.map((s) => s.node.language))].sort();
   const mode = opts.dryRun ? "dry-run" : opts.apply ? "apply" : "patch-only";
@@ -4228,7 +4394,7 @@ var CLAUDE_SKILL_CONFIG = {
       command: "npx",
       args: ["-y", "@neat.is/mcp"],
       env: {
-        NEAT_API_URL: "http://localhost:8080"
+        NEAT_CORE_URL: "http://localhost:8080"
       }
     }
   }
@@ -4274,6 +4440,9 @@ async function runSkill(opts) {
   console.log("");
   console.log("Manual install: copy mcpServers.neat from --print-config into ~/.claude.json,");
   console.log("then restart Claude Code. See packages/claude-skill/SKILL.md for the tool list.");
+  console.log("");
+  console.log("The MCP server reads NEAT_CORE_URL for the daemon URL \u2014 point it at a");
+  console.log("non-default daemon by editing that value in the generated config.");
   return { exitCode: 0 };
 }
 async function main() {
@@ -4375,16 +4544,14 @@ async function main() {
     process.on("SIGINT", shutdown);
     return;
   }
-  if (cmd === "list") {
-    const projects = await listProjects();
-    if (projects.length === 0) {
-      console.log("no projects registered. run `neat init <path>` to register one.");
+  if (cmd === "list" || cmd === "ps") {
+    const rows = await listMachineProjects();
+    if (rows.length === 0) {
+      console.log("no daemons running and no projects registered. run `neat init <path>` to register one.");
       return;
     }
-    for (const p of projects) {
-      const seen = p.lastSeenAt ? p.lastSeenAt : "never";
-      const langs = p.languages.length > 0 ? p.languages.join(",") : "-";
-      console.log(`${p.name}	${p.status}	${langs}	${p.path}	last-seen=${seen}`);
+    for (const r of rows) {
+      console.log(formatMachineProjectRow(r));
     }
     return;
   }
@@ -4395,6 +4562,15 @@ async function main() {
       usage();
       process.exit(2);
     }
+    const daemon = await findDaemonByProject(name);
+    if (daemon) {
+      if (daemon.live && signalDaemonStop(daemon.record.pid)) {
+        console.log(`paused: ${name} (${daemon.record.projectPath}) \u2014 stopped daemon pid ${daemon.record.pid}`);
+      } else {
+        console.log(`paused: ${name} (${daemon.record.projectPath}) \u2014 daemon was not running`);
+      }
+      return;
+    }
     try {
       const entry2 = await setStatus(name, "paused");
       console.log(`paused: ${entry2.name} (${entry2.path})`);
@@ -4411,6 +4587,15 @@ async function main() {
       usage();
       process.exit(2);
     }
+    const daemon = await findDaemonByProject(name);
+    if (daemon) {
+      if (daemon.live) {
+        console.log(`resume: ${name} (${daemon.record.projectPath}) \u2014 daemon already running`);
+      } else {
+        console.log(`resume: ${name} (${daemon.record.projectPath}) \u2014 run \`neat ${daemon.record.projectPath}\` to start its daemon again`);
+      }
+      return;
+    }
     try {
       const entry2 = await setStatus(name, "active");
       console.log(`resumed: ${entry2.name} (${entry2.path})`);
@@ -4432,15 +4617,36 @@ async function main() {
       usage();
       process.exit(2);
     }
+    const daemon = await findDaemonByProject(name);
     const removed = await removeProject(name);
-    if (!removed) {
+    if (!daemon && !removed) {
       console.error(`neat uninstall: no project named "${name}"`);
       process.exit(1);
     }
-    console.log(`unregistered: ${removed.name} (${removed.path})`);
+    const projectPath2 = daemon?.record.projectPath ?? removed?.path ?? "(unknown path)";
+    if (daemon) {
+      if (daemon.live && signalDaemonStop(daemon.record.pid)) {
+        console.log(`uninstall: ${name} \u2014 stopped daemon pid ${daemon.record.pid}`);
+      }
+      await removeDaemonRecord(daemon.source);
+    }
+    console.log(`unregistered: ${name} (${projectPath2})`);
     console.log("note: neat-out/, policy.json, and other files at the project path were left in place.");
     return;
   }
+  if (cmd === "prune") {
+    const removed = await pruneRegistry({ ttlMs: 0 });
+    if (parsed.json) {
+      console.log(JSON.stringify(removed.map((p) => ({ name: p.name, path: p.path })), null, 2));
+      return;
+    }
+    if (removed.length === 0) {
+      console.log("nothing to prune \u2014 every registered project path still exists.");
+      return;
+    }
+    console.log(`pruned ${removed.length} project${removed.length === 1 ? "" : "s"}: ${removed.map((p) => p.name).join(", ")}`);
+    return;
+  }
   if (cmd === "deploy") {
     const artifact = await runDeploy();
     const block = renderOtelEnvBlock2(artifact.token);
@@ -4528,12 +4734,44 @@ function resolveProjectFlag(parsed) {
   if (env && env.length > 0 && env !== DEFAULT_PROJECT) return env;
   return void 0;
 }
+var ProjectResolutionError = class extends Error {
+  constructor(message, exitCode = 2) {
+    super(message);
+    this.exitCode = exitCode;
+    this.name = "ProjectResolutionError";
+  }
+  exitCode;
+};
+async function resolveProjectForVerb(client, parsed) {
+  const explicit = resolveProjectFlag(parsed);
+  if (explicit) return explicit;
+  const projects = await client.get("/projects");
+  if (projects.some((p) => p.name === DEFAULT_PROJECT)) {
+    return void 0;
+  }
+  if (projects.length === 1) {
+    return projects[0].name;
+  }
+  if (projects.length === 0) {
+    throw new ProjectResolutionError(
+      "No projects are registered with the daemon yet. Run `npx neat.is` in a repo to build a graph first, then re-run this command."
+    );
+  }
+  const names = projects.map((p) => p.name).sort().map((n) => `  ${n}`).join("\n");
+  throw new ProjectResolutionError(
+    `Several projects are registered and none is named "default", so I can't pick one for you.
+Pass --project <name> to choose:
+${names}`
+  );
+}
+function resolveDaemonUrl() {
+  return process.env.NEAT_API_URL ?? process.env.NEAT_CORE_URL ?? "http://localhost:8080";
+}
 async function runQueryVerb(cmd, parsed) {
-  const baseUrl = process.env.NEAT_API_URL ?? "http://localhost:8080";
+  const baseUrl = resolveDaemonUrl();
   const client = createHttpClient(baseUrl, resolveAuthToken());
-  const project = resolveProjectFlag(parsed);
   const positional = parsed.positional;
-  let work;
+  let makeWork;
   switch (cmd) {
     case "root-cause": {
       const node = positional[0];
@@ -4541,7 +4779,7 @@ async function runQueryVerb(cmd, parsed) {
         console.error("neat root-cause: missing <node-id>");
         return 2;
       }
-      work = runRootCause(client, {
+      makeWork = (project) => runRootCause(client, {
         errorNode: node,
         ...parsed.errorId ? { errorId: parsed.errorId } : {},
         ...project ? { project } : {}
@@ -4554,7 +4792,7 @@ async function runQueryVerb(cmd, parsed) {
         console.error("neat blast-radius: missing <node-id>");
         return 2;
       }
-      work = runBlastRadius(client, {
+      makeWork = (project) => runBlastRadius(client, {
         nodeId: node,
         ...parsed.depth !== null ? { depth: parsed.depth } : {},
         ...project ? { project } : {}
@@ -4567,7 +4805,7 @@ async function runQueryVerb(cmd, parsed) {
         console.error("neat dependencies: missing <node-id>");
         return 2;
       }
-      work = runDependencies(client, {
+      makeWork = (project) => runDependencies(client, {
         nodeId: node,
         ...parsed.depth !== null ? { depth: parsed.depth } : {},
         ...project ? { project } : {}
@@ -4580,14 +4818,14 @@ async function runQueryVerb(cmd, parsed) {
         console.error("neat observed-dependencies: missing <node-id>");
         return 2;
       }
-      work = runObservedDependencies(client, {
+      makeWork = (project) => runObservedDependencies(client, {
         nodeId: node,
         ...project ? { project } : {}
       });
       break;
     }
     case "incidents": {
-      work = runIncidents(client, {
+      makeWork = (project) => runIncidents(client, {
         ...positional[0] ? { nodeId: positional[0] } : {},
         ...parsed.limit !== null ? { limit: parsed.limit } : {},
         ...project ? { project } : {}
@@ -4600,7 +4838,7 @@ async function runQueryVerb(cmd, parsed) {
         console.error("neat search: missing <query>");
         return 2;
       }
-      work = runSearch(client, { query: q, ...project ? { project } : {} });
+      makeWork = (project) => runSearch(client, { query: q, ...project ? { project } : {} });
       break;
     }
     case "diff": {
@@ -4609,14 +4847,14 @@ async function runQueryVerb(cmd, parsed) {
         console.error("neat diff: --against <snapshot-path> is required");
         return 2;
       }
-      work = runDiff(client, {
+      makeWork = (project) => runDiff(client, {
         againstSnapshot: against,
         ...project ? { project } : {}
       });
       break;
     }
     case "stale-edges": {
-      work = runStaleEdges(client, {
+      makeWork = (project) => runStaleEdges(client, {
         ...parsed.limit !== null ? { limit: parsed.limit } : {},
         ...parsed.edgeType ? { edgeType: parsed.edgeType } : {},
         ...project ? { project } : {}
@@ -4635,7 +4873,7 @@ async function runQueryVerb(cmd, parsed) {
           return 2;
         }
       }
-      work = runPolicies(client, {
+      makeWork = (project) => runPolicies(client, {
         ...parsed.node ? { nodeId: parsed.node } : {},
         ...hypothetical ? { hypotheticalAction: hypothetical } : {},
         ...project ? { project } : {}
@@ -4659,7 +4897,7 @@ async function runQueryVerb(cmd, parsed) {
         }
         typeFilter = out;
       }
-      work = runDivergences(client, {
+      makeWork = (project) => runDivergences(client, {
         ...typeFilter ? { type: typeFilter } : {},
         ...parsed.minConfidence !== null ? { minConfidence: parsed.minConfidence } : {},
         ...parsed.node ? { node: parsed.node } : {},
@@ -4672,16 +4910,21 @@ async function runQueryVerb(cmd, parsed) {
       return 2;
   }
   try {
-    const result = await work;
+    const project = await resolveProjectForVerb(client, parsed);
+    const result = await makeWork(project);
     if (parsed.json) process.stdout.write(formatJson(result) + "\n");
     else process.stdout.write(formatHuman(result) + "\n");
     return 0;
   } catch (err) {
+    if (err instanceof ProjectResolutionError) {
+      console.error(`neat ${cmd}: ${err.message}`);
+      return err.exitCode;
+    }
     if (err instanceof HttpError) {
       const detail = err.responseBody.length > 0 ? err.responseBody : err.message;
       console.error(`neat ${cmd}: ${detail.trim()}`);
     } else if (err instanceof TransportError) {
-      console.error(`neat ${cmd}: ${err.message}. Is the daemon running? (NEAT_API_URL=${process.env.NEAT_API_URL ?? "http://localhost:8080"})`);
+      console.error(`neat ${cmd}: ${err.message}. Is the daemon running? (NEAT_API_URL=${resolveDaemonUrl()})`);
     } else {
       console.error(`neat ${cmd}: ${err.message}`);
     }
@@ -4697,6 +4940,7 @@ if (/[\\/]cli\.(?:cjs|js)$/.test(entry) || entry.endsWith("/cli") || entry.endsW
 }
 export {
   CLAUDE_SKILL_CONFIG,
+  ProjectResolutionError,
   QUERY_VERBS,
   commandPrefix,
   isNpxInvocation,
@@ -4704,6 +4948,7 @@ export {
   parseArgs,
   printBanner,
   readPackageVersion,
+  resolveProjectForVerb,
   runInit,
   runQueryVerb,
   runSkill,