facult 1.2.1 → 1.3.0

package/README.md

@@ -104,7 +104,7 @@ Put that in `config.toml` or `config.local.toml` under the active canonical root
 
 - canonical source lives in `~/.ai` or `<repo>/.ai`
 - rendered outputs live in tool homes like `~/.codex`, `<repo>/.codex`, `~/.claude`, or `~/.cursor`
-- generated state lives in `~/.facult` or `<repo>/.facult`
+- generated Facult-owned state lives in `~/.ai/.facult` or `<repo>/.ai/.facult`
 
 This keeps authored capability portable and reviewable while still producing the exact files each tool expects.
 
@@ -217,9 +217,9 @@ facult index
 
 Why `keep-current`: it is deterministic and non-interactive for duplicate sources.
 
-Canonical source root: `~/.ai` for global work, or `<repo>/.ai` for project-local work. Generated state lives next to the active canonical root:
-- global: `~/.facult`
-- project: `<repo>/.facult`
+Canonical source root: `~/.ai` for global work, or `<repo>/.ai` for project-local work. Facult-owned generated/config/runtime state lives inside the active canonical root:
+- global: `~/.ai/.facult`
+- project: `<repo>/.ai/.facult`
 
 ### 3b. Bootstrap a repo-local `.ai`
 
@@ -229,7 +229,7 @@ bunx facult templates init project-ai
 bunx facult index
 ```
 
-This seeds `<repo>/.ai` from the built-in Facult operating-model pack and writes a merged project index/graph under `<repo>/.facult/ai/`.
+This seeds `<repo>/.ai` from the built-in Facult operating-model pack and writes a merged project index/graph under `<repo>/.ai/.facult/ai/`.
 
 ### 4. Inspect what you have
 
@@ -365,19 +365,19 @@ Typical layout:
     agents/
     skills/
     tools/
-  .facult/
-    ai/
-      index.json
-      graph.json
+    .facult/
+      ai/
+        index.json
+        graph.json
   .codex/
   .claude/
 ```
 
 Important split:
 - `.ai/` is canonical source
-- `.facult/` is generated state, trust state, managed tool state, autosync state, and caches
+- `.ai/.facult/` is Facult-owned generated state, trust state, managed tool state, autosync state, and caches
 - tool homes such as `.codex/` and `.claude/` are rendered outputs
-- the generated capability graph lives at `.facult/ai/graph.json`
+- the generated capability graph lives at `.ai/.facult/ai/graph.json`
 
 ### Asset types
 
@@ -408,11 +408,9 @@ Not every asset syncs directly to a tool. Some exist primarily to support render
 
 Canonical render context is layered explicitly:
 1. built-ins injected by `facult`
-2. `~/.ai/config.toml`
-3. `~/.ai/config.local.toml`
-4. `~/.ai/projects/<slug>/config.toml`
-5. `~/.ai/projects/<slug>/config.local.toml`
-6. explicit runtime overrides
+2. active canonical root `config.toml`
+3. active canonical root `config.local.toml`
+4. explicit runtime overrides
 
 Built-ins currently include:
 - `AI_ROOT`
@@ -423,8 +421,8 @@ Built-ins currently include:
 - `TARGET_PATH`
 
 Recommended split:
-- `config.toml`: tracked, portable, non-secret refs/defaults
-- `config.local.toml`: ignored, machine-local paths and secrets
+- `~/.ai/config.toml` or `<repo>/.ai/config.toml`: tracked, portable, non-secret refs/defaults
+- `~/.ai/config.local.toml` or `<repo>/.ai/config.local.toml`: ignored, machine-local paths and secrets
 - `[builtin].sync_defaults = false`: disable builtin default sync/materialization for this root
 - `facult sync --builtin-conflicts overwrite`: allow packaged builtin defaults to overwrite locally modified generated targets
 
@@ -453,7 +451,7 @@ Snippets are already used during global Codex `AGENTS.md` rendering.
 
 ### Graph inspection
 
-The generated graph in `.facult/ai/graph.json` is queryable directly:
+The generated graph in `.ai/.facult/ai/graph.json` is queryable directly:
 
 ```bash
 facult graph show instruction:WRITING
@@ -496,13 +494,13 @@ facult ai evolve apply EV-00001
 facult ai evolve promote EV-00003 --to global --project
 ```
 
-Runtime state stays generated and local:
-- global writeback state: `~/.facult/ai/global/...`
-- project writeback state: `~/.facult/ai/projects/<slug>/...`
+Runtime state stays generated and local inside the active canonical root:
+- global writeback state: `~/.ai/.facult/ai/global/...`
+- project writeback state: `<repo>/.ai/.facult/ai/project/...`
 
 That split is intentional:
 - canonical source remains in `~/.ai` or `<repo>/.ai`
-- writeback queues, journals, and proposal records stay outside the canonical git-backed tree by default
+- writeback queues, journals, proposal records, trust state, autosync state, and other Facult-owned runtime/config state stay inside `.ai/.facult/` rather than inside the tool homes
 
 Use writeback when:
 - a task exposed a weak or misleading verification loop
@@ -652,7 +650,7 @@ facult <command> --help
 `facult` resolves the canonical root in this order:
 1. `FACULT_ROOT_DIR`
 2. nearest project `.ai` from the current working directory for CLI-facing commands
-3. `~/.facult/config.json` (`rootDir`)
+3. `~/.ai/.facult/config.json` (`rootDir`)
 4. `~/.ai`
 5. `~/agents/.facult` (or a detected legacy store under `~/agents/`)
 
@@ -660,12 +658,12 @@ facult <command> --help
 
 - `FACULT_ROOT_DIR`: override canonical store location
 - `FACULT_VERSION`: version selector for `scripts/install.sh` (`latest` by default)
-- `FACULT_INSTALL_DIR`: install target dir for `scripts/install.sh` (`~/.facult/bin` by default)
+- `FACULT_INSTALL_DIR`: install target dir for `scripts/install.sh` (`~/.ai/.facult/bin` by default)
 - `FACULT_INSTALL_PM`: force package manager detection for npm bootstrap launcher (`npm` or `bun`)
 
 ### State and report files
 
-Under `~/.facult/`:
+Under `~/.ai/.facult/`:
 - `sources.json` (latest inventory scan state)
 - `consolidated.json` (consolidation state)
 - `managed.json` (managed tool state)
@@ -679,7 +677,7 @@ Under `~/.facult/`:
 
 ### Config reference
 
-`~/.facult/config.json` supports:
+`~/.ai/.facult/config.json` supports:
 - `rootDir`
 - `scanFrom`
 - `scanFromIgnore`
@@ -710,7 +708,7 @@ Default source aliases:
 - `skills.sh`
 - `clawhub`
 
-Custom remote sources can be defined in `~/.facult/indices.json` (manifest URL, optional integrity, optional signature keys/signature verification settings).
+Custom remote sources can be defined in `~/.ai/.facult/indices.json` (manifest URL, optional integrity, optional signature keys/signature verification settings).
 
 ## Local Install Modes
 
@@ -722,7 +720,7 @@ bun run install:bin
 bun run install:status
 ```
 
-Default install path is `~/.facult/bin/facult`. You can pass a custom target dir via `--dir=/path`.
+Default install path is `~/.ai/.facult/bin/facult`. You can pass a custom target dir via `--dir=/path`.
 
 ## Autosync
 
@@ -780,7 +778,7 @@ Release behavior:
 3. The same release workflow then builds platform binaries and uploads them to that GitHub release.
 4. npm publish runs only after binary asset upload succeeds (`publish-npm` depends on `publish-assets`).
 5. Published release assets include platform binaries, `facult-install.sh`, and `SHA256SUMS`.
-6. The npm package launcher resolves your platform, downloads the matching release binary, caches it under `~/.facult/runtime/<version>/<platform-arch>/`, and runs it.
+6. The npm package launcher resolves your platform, downloads the matching release binary, caches it under `~/.ai/.facult/runtime/<version>/<platform-arch>/`, and runs it.
 
 Current prebuilt binary targets:
 - `darwin-x64`

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "facult",
-  "version": "1.2.1",
+  "version": "1.3.0",
   "description": "Manage coding-agent skills and MCP configs across tools.",
   "type": "module",
   "license": "MIT",

package/src/ai-state.ts

@@ -1,7 +1,11 @@
 import { copyFile, mkdir, stat } from "node:fs/promises";
 import { dirname, join } from "node:path";
 import { buildIndex } from "./index-builder";
-import { facultAiGraphPath, facultAiIndexPath } from "./paths";
+import {
+  facultAiGraphPath,
+  facultAiIndexPath,
+  legacyFacultStateDirForRoot,
+} from "./paths";
 
 async function fileExists(path: string): Promise<boolean> {
   try {
@@ -15,6 +19,22 @@ export function legacyAiIndexPath(rootDir: string): string {
   return join(rootDir, "index.json");
 }
 
+function legacyGeneratedAiIndexPath(homeDir: string, rootDir: string): string {
+  return join(
+    legacyFacultStateDirForRoot(rootDir, homeDir),
+    "ai",
+    "index.json"
+  );
+}
+
+function legacyGeneratedAiGraphPath(homeDir: string, rootDir: string): string {
+  return join(
+    legacyFacultStateDirForRoot(rootDir, homeDir),
+    "ai",
+    "graph.json"
+  );
+}
+
 export async function ensureAiIndexPath(args: {
   homeDir: string;
   rootDir: string;
@@ -29,6 +49,22 @@ export async function ensureAiIndexPath(args: {
     return { path: generatedPath, repaired: false, source: "generated" };
   }
 
+  const legacyGeneratedPath = legacyGeneratedAiIndexPath(
+    args.homeDir,
+    args.rootDir
+  );
+  if (await fileExists(legacyGeneratedPath)) {
+    if (args.repair !== false) {
+      await mkdir(dirname(generatedPath), { recursive: true });
+      await copyFile(legacyGeneratedPath, generatedPath);
+    }
+    return {
+      path: generatedPath,
+      repaired: args.repair !== false,
+      source: "legacy",
+    };
+  }
+
   const legacyPath = legacyAiIndexPath(args.rootDir);
   if (await fileExists(legacyPath)) {
     if (args.repair !== false) {
@@ -67,6 +103,18 @@ export async function ensureAiGraphPath(args: {
     return { path: generatedPath, rebuilt: false };
   }
 
+  const legacyGeneratedPath = legacyGeneratedAiGraphPath(
+    args.homeDir,
+    args.rootDir
+  );
+  if (await fileExists(legacyGeneratedPath)) {
+    if (args.repair !== false) {
+      await mkdir(dirname(generatedPath), { recursive: true });
+      await copyFile(legacyGeneratedPath, generatedPath);
+    }
+    return { path: generatedPath, rebuilt: args.repair !== false };
+  }
+
   if (args.repair !== false) {
     const { graphPath } = await buildIndex({
       rootDir: args.rootDir,

package/src/audit/agent.ts

@@ -1,7 +1,7 @@
 import { mkdir, mkdtemp } from "node:fs/promises";
 import { homedir, tmpdir } from "node:os";
 import { basename, join, sep } from "node:path";
-import { facultRootDir, readFacultConfig } from "../paths";
+import { facultRootDir, facultStateDir, readFacultConfig } from "../paths";
 import type { AssetFile, ScanResult } from "../scan";
 import { scan } from "../scan";
 import {
@@ -978,7 +978,7 @@ export async function runAgentAudit(opts?: {
     },
   };
 
-  const auditDir = join(home, ".facult", "audit");
+  const auditDir = join(facultStateDir(home), "audit");
   await mkdir(auditDir, { recursive: true });
   await Bun.write(
     join(auditDir, "agent-latest.json"),
@@ -1040,7 +1040,7 @@ function printHuman(report: AgentAuditReport) {
     `By severity: critical=${report.summary.bySeverity.critical}, high=${report.summary.bySeverity.high}, medium=${report.summary.bySeverity.medium}, low=${report.summary.bySeverity.low}`
   );
   console.log(
-    `Wrote ${join(homedir(), ".facult", "audit", "agent-latest.json")}`
+    `Wrote ${join(facultStateDir(homedir()), "audit", "agent-latest.json")}`
   );
 }
 

package/src/audit/static.ts

@@ -2,7 +2,7 @@ import { mkdir } from "node:fs/promises";
 import { homedir } from "node:os";
 import { basename, join } from "node:path";
 import { parse as parseYaml } from "yaml";
-import { readFacultConfig } from "../paths";
+import { facultStateDir, readFacultConfig } from "../paths";
 import type { ScanResult } from "../scan";
 import { scan } from "../scan";
 import {
@@ -649,7 +649,7 @@ export async function runStaticAudit(opts?: {
   const argv = opts?.argv ?? [];
   const home = opts?.homeDir ?? homedir();
   const rulesPath =
-    opts?.rulesPath ?? join(home, ".facult", "audit-rules.yaml");
+    opts?.rulesPath ?? join(facultStateDir(home), "audit-rules.yaml");
 
   const overrides = await loadRuleOverrides(rulesPath);
   const rules = compileRules(mergeRules(DEFAULT_RULES, overrides));
@@ -1040,7 +1040,7 @@ export async function runStaticAudit(opts?: {
     },
   };
 
-  const auditDir = join(home, ".facult", "audit");
+  const auditDir = join(facultStateDir(home), "audit");
   await ensureDir(auditDir);
   await Bun.write(
     join(auditDir, "static-latest.json"),
@@ -1091,7 +1091,7 @@ function printHuman(report: StaticAuditReport) {
     `By severity: critical=${report.summary.bySeverity.critical}, high=${report.summary.bySeverity.high}, medium=${report.summary.bySeverity.medium}, low=${report.summary.bySeverity.low}`
   );
   console.log(
-    `Wrote ${join(homedir(), ".facult", "audit", "static-latest.json")}`
+    `Wrote ${join(facultStateDir(homedir()), "audit", "static-latest.json")}`
   );
 }
 

package/src/audit/tui.ts

@@ -12,7 +12,7 @@ import {
   text,
 } from "@clack/prompts";
 import { buildIndex } from "../index-builder";
-import { facultRootDir, readFacultConfig } from "../paths";
+import { facultRootDir, facultStateDir, readFacultConfig } from "../paths";
 import { type QuarantineMode, quarantineItems } from "../quarantine";
 import { type AgentAuditReport, runAgentAudit } from "./agent";
 import { runStaticAudit } from "./static";
@@ -206,7 +206,7 @@ Usage:
 
 Notes:
   - This is an interactive wizard (TTY required).
-  - Quarantine will move/copy files into ~/.facult/quarantine/<timestamp>/ and write a manifest.json.
+  - Quarantine will move/copy files into ~/.ai/.facult/quarantine/<timestamp>/ and write a manifest.json.
   - For non-interactive runs, use: facult audit --non-interactive ...
 `);
 }
@@ -228,7 +228,7 @@ export async function auditTuiCommand(argv: string[]) {
   if (cfgRoots.length) {
     note(
       `Configured scanFrom roots:\n- ${cfgRoots.join("\n- ")}`,
-      "~/.facult/config.json"
+      "~/.ai/.facult/config.json"
     );
   }
 
@@ -285,7 +285,7 @@ export async function auditTuiCommand(argv: string[]) {
             {
               value: "config",
               label: "Use configured scanFrom",
-              hint: "from ~/.facult/config.json",
+              hint: "from ~/.ai/.facult/config.json",
             },
           ]
         : []),
@@ -448,13 +448,13 @@ export async function auditTuiCommand(argv: string[]) {
   if (reports.static) {
     summaries.push(`Static: ${summarizeReportStatic(reports.static)}`);
     summaries.push(
-      `Wrote ${join(homedir(), ".facult", "audit", "static-latest.json")}`
+      `Wrote ${join(facultStateDir(homedir()), "audit", "static-latest.json")}`
     );
   }
   if (reports.agent) {
     summaries.push(`Agent: ${summarizeReportAgent(reports.agent)}`);
     summaries.push(
-      `Wrote ${join(homedir(), ".facult", "audit", "agent-latest.json")}`
+      `Wrote ${join(facultStateDir(homedir()), "audit", "agent-latest.json")}`
     );
   }
   if (summaries.length) {
@@ -524,7 +524,7 @@ export async function auditTuiCommand(argv: string[]) {
         {
           value: "quarantine",
           label: "Quarantine items",
-          hint: "move/copy to ~/.facult/quarantine",
+          hint: "move/copy to ~/.ai/.facult/quarantine",
         },
         { value: "view", label: "View item details", hint: "inspect findings" },
         { value: "exit", label: "Exit", hint: "leave files unchanged" },
@@ -617,7 +617,7 @@ export async function auditTuiCommand(argv: string[]) {
 
     const ts = new Date().toISOString();
     const stamp = ts.replace(/[:.]/g, "-");
-    const destDir = join(homedir(), ".facult", "quarantine", stamp);
+    const destDir = join(facultStateDir(homedir()), "quarantine", stamp);
 
     const plan = await quarantineItems({
       items,

package/src/autosync.ts

@@ -4,7 +4,12 @@ import { homedir, hostname } from "node:os";
 import { basename, dirname, join } from "node:path";
 import { parseCliContextArgs, resolveCliContextRoot } from "./cli-context";
 import { syncManagedTools } from "./manage";
-import { facultRootDir, facultStateDir, projectRootFromAiRoot } from "./paths";
+import {
+  facultRootDir,
+  facultStateDir,
+  legacyFacultStateDirForRoot,
+  projectRootFromAiRoot,
+} from "./paths";
 
 const AUTOSYNC_VERSION = 1 as const;
 const DEFAULT_DEBOUNCE_MS = 1500;
@@ -94,20 +99,33 @@ function runDetached(context: string, promise: Promise<void>) {
   });
 }
 
-function autosyncDir(home: string): string {
-  return join(facultStateDir(home), "autosync");
+function autosyncDir(home: string, rootDir?: string): string {
+  return join(facultStateDir(home, rootDir), "autosync");
 }
 
-function autosyncServicesDir(home: string): string {
-  return join(autosyncDir(home), "services");
+function legacyAutosyncDir(home: string, rootDir?: string): string {
+  const resolvedRoot = rootDir ?? facultRootDir(home);
+  return join(legacyFacultStateDirForRoot(resolvedRoot, home), "autosync");
 }
 
-function autosyncStateDir(home: string): string {
-  return join(autosyncDir(home), "state");
+function autosyncServicesDir(home: string, rootDir?: string): string {
+  return join(autosyncDir(home, rootDir), "services");
 }
 
-function autosyncLogsDir(home: string): string {
-  return join(autosyncDir(home), "logs");
+function legacyAutosyncServicesDir(home: string, rootDir?: string): string {
+  return join(legacyAutosyncDir(home, rootDir), "services");
+}
+
+function autosyncStateDir(home: string, rootDir?: string): string {
+  return join(autosyncDir(home, rootDir), "state");
+}
+
+function legacyAutosyncStateDir(home: string, rootDir?: string): string {
+  return join(legacyAutosyncDir(home, rootDir), "state");
+}
+
+function autosyncLogsDir(home: string, rootDir?: string): string {
+  return join(autosyncDir(home, rootDir), "logs");
 }
 
 function serviceSuffix(
@@ -151,12 +169,36 @@ function autosyncPlistPath(home: string, serviceName: string): string {
   );
 }
 
-function autosyncConfigPath(home: string, serviceName: string): string {
-  return join(autosyncServicesDir(home), `${serviceName}.json`);
+function autosyncConfigPath(
+  home: string,
+  serviceName: string,
+  rootDir?: string
+): string {
+  return join(autosyncServicesDir(home, rootDir), `${serviceName}.json`);
+}
+
+function legacyAutosyncConfigPath(
+  home: string,
+  serviceName: string,
+  rootDir?: string
+): string {
+  return join(legacyAutosyncServicesDir(home, rootDir), `${serviceName}.json`);
+}
+
+function autosyncRuntimeStatePath(
+  home: string,
+  serviceName: string,
+  rootDir?: string
+): string {
+  return join(autosyncStateDir(home, rootDir), `${serviceName}.json`);
 }
 
-function autosyncRuntimeStatePath(home: string, serviceName: string): string {
-  return join(autosyncStateDir(home), `${serviceName}.json`);
+function legacyAutosyncRuntimeStatePath(
+  home: string,
+  serviceName: string,
+  rootDir?: string
+): string {
+  return join(legacyAutosyncStateDir(home, rootDir), `${serviceName}.json`);
 }
 
 function escapeXml(value: string): string {
@@ -204,7 +246,7 @@ export function buildLaunchAgentSpec(args: {
   const { homeDir, rootDir, serviceName } = args;
   const label = autosyncLabel(serviceName);
   const invocation = args.invocation ?? resolveAutosyncInvocation();
-  const logsDir = autosyncLogsDir(homeDir);
+  const logsDir = autosyncLogsDir(homeDir, rootDir);
 
   return {
     label,
@@ -281,34 +323,58 @@ async function writeJsonFile(pathValue: string, data: unknown): Promise<void> {
 
 export async function loadAutosyncConfig(
   serviceName: string,
-  homeDir: string = homedir()
+  homeDir: string = homedir(),
+  rootDir?: string
 ): Promise<AutosyncServiceConfig | null> {
-  return await readJsonFile<AutosyncServiceConfig>(
-    autosyncConfigPath(homeDir, serviceName)
-  );
+  const candidates = [
+    autosyncConfigPath(homeDir, serviceName, rootDir),
+    legacyAutosyncConfigPath(homeDir, serviceName, rootDir),
+  ];
+  for (const candidate of candidates) {
+    const config = await readJsonFile<AutosyncServiceConfig>(candidate);
+    if (config) {
+      return config;
+    }
+  }
+  return null;
 }
 
 async function saveAutosyncConfig(
   config: AutosyncServiceConfig,
   homeDir: string
 ): Promise<void> {
-  await writeJsonFile(autosyncConfigPath(homeDir, config.name), config);
+  await writeJsonFile(
+    autosyncConfigPath(homeDir, config.name, config.rootDir),
+    config
+  );
 }
 
 export async function loadAutosyncRuntimeState(
   serviceName: string,
-  homeDir: string = homedir()
+  homeDir: string = homedir(),
+  rootDir?: string
 ): Promise<AutosyncRuntimeState | null> {
-  return await readJsonFile<AutosyncRuntimeState>(
-    autosyncRuntimeStatePath(homeDir, serviceName)
-  );
+  const candidates = [
+    autosyncRuntimeStatePath(homeDir, serviceName, rootDir),
+    legacyAutosyncRuntimeStatePath(homeDir, serviceName, rootDir),
+  ];
+  for (const candidate of candidates) {
+    const state = await readJsonFile<AutosyncRuntimeState>(candidate);
+    if (state) {
+      return state;
+    }
+  }
+  return null;
 }
 
 async function saveAutosyncRuntimeState(
   state: AutosyncRuntimeState,
   homeDir: string
 ): Promise<void> {
-  await writeJsonFile(autosyncRuntimeStatePath(homeDir, state.service), state);
+  await writeJsonFile(
+    autosyncRuntimeStatePath(homeDir, state.service, state.rootDir),
+    state
+  );
 }
 
 async function runCommand(
@@ -535,7 +601,7 @@ export async function runAutosyncService(
 
   const persistState = async (patch: Partial<AutosyncRuntimeState>) => {
     const current =
-      (await loadAutosyncRuntimeState(config.name, home)) ??
+      (await loadAutosyncRuntimeState(config.name, home, config.rootDir)) ??
       ({
         version: AUTOSYNC_VERSION,
         service: config.name,
@@ -778,7 +844,7 @@ export async function installAutosyncService(args: {
   const plist = buildLaunchAgentPlist(spec);
 
   await mkdir(dirname(spec.plistPath), { recursive: true });
-  await mkdir(autosyncLogsDir(home), { recursive: true });
+  await mkdir(autosyncLogsDir(home, rootDir), { recursive: true });
   await saveAutosyncConfig(config, home);
   await writeFile(spec.plistPath, plist, "utf8");
 
@@ -804,14 +870,30 @@ export async function uninstallAutosyncService(args: {
 
   await runLaunchctl(["bootout", `${domain}/${label}`]).catch(() => null);
   await rm(autosyncPlistPath(home, serviceName), { force: true });
-  await rm(autosyncConfigPath(home, serviceName), { force: true });
+  await rm(autosyncConfigPath(home, serviceName, rootDir), { force: true });
 }
 
 export async function repairAutosyncServices(
-  homeDir: string = homedir()
+  homeDir: string = homedir(),
+  rootDir?: string
 ): Promise<boolean> {
-  const servicesDir = autosyncServicesDir(homeDir);
-  const files = await readdir(servicesDir).catch(() => [] as string[]);
+  const activeRoot = rootDir ?? facultRootDir(homeDir);
+  const serviceDirs = [
+    autosyncServicesDir(homeDir, activeRoot),
+    legacyAutosyncServicesDir(homeDir, activeRoot),
+  ];
+  const seen = new Set<string>();
+  const files: string[] = [];
+  for (const dir of serviceDirs) {
+    const entries = await readdir(dir).catch(() => [] as string[]);
+    for (const entry of entries) {
+      if (seen.has(entry)) {
+        continue;
+      }
+      seen.add(entry);
+      files.push(entry);
+    }
+  }
   let changed = false;
 
   for (const entry of files) {
@@ -819,7 +901,7 @@ export async function repairAutosyncServices(
       continue;
     }
     const serviceName = basename(entry, ".json");
-    const config = await loadAutosyncConfig(serviceName, homeDir);
+    const config = await loadAutosyncConfig(serviceName, homeDir, activeRoot);
     if (!config) {
       continue;
     }
@@ -843,7 +925,9 @@ export async function repairAutosyncServices(
     );
     if (currentText !== desired) {
       await mkdir(dirname(spec.plistPath), { recursive: true });
-      await mkdir(autosyncLogsDir(homeDir), { recursive: true });
+      await mkdir(autosyncLogsDir(homeDir, config.rootDir), {
+        recursive: true,
+      });
       await writeFile(spec.plistPath, desired, "utf8");
       const domain = launchdDomain();
       await runLaunchctl(["bootout", `${domain}/${spec.label}`]).catch(
@@ -872,8 +956,8 @@ export async function autosyncStatus(args: {
     args.rootDir ??
     resolveCliContextRoot({ homeDir: home, cwd: process.cwd() });
   const serviceName = autosyncServiceName(args.tool, rootDir, home);
-  const config = await loadAutosyncConfig(serviceName, home);
-  const state = await loadAutosyncRuntimeState(serviceName, home);
+  const config = await loadAutosyncConfig(serviceName, home, rootDir);
+  const state = await loadAutosyncRuntimeState(serviceName, home, rootDir);
   const plistPath = autosyncPlistPath(home, serviceName);
   const plistExists = await pathExists(plistPath);
   const label = autosyncLabel(serviceName);