opencode-autoresearch 3.3.1 → 3.4.1

package/dist/index.d.ts

@@ -1,7 +1,24 @@
 import { VERSION, PACKAGE_NAME, PRODUCT_BRAND, SKILL_NAME } from "./constants.js";
 export declare const id = "autoresearch";
 export declare const repoRoot: string;
-export declare const version = "3.3.1";
+export declare const version = "3.4.1";
+type OpenCodeConfig = {
+    command?: Record<string, {
+        template: string;
+    }>;
+    skills?: {
+        paths?: string[];
+    };
+};
+export declare function server(): Promise<{
+    config(config: OpenCodeConfig): void;
+    event(): undefined;
+}>;
+declare const _default: {
+    id: string;
+    server: typeof server;
+};
+export default _default;
 export { VERSION, PACKAGE_NAME, PRODUCT_BRAND, SKILL_NAME };
 export type { RunConfig, WizardConfig, Metric, RunStats, RunFlags, LastIteration, RunState, SupervisorSnapshot, LabelRequirements, ArtifactPaths, } from "./types.js";
 //# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAGA,OAAO,EACL,OAAO,EACP,YAAY,EACZ,aAAa,EACb,UAAU,EACX,MAAM,gBAAgB,CAAC;AAIxB,eAAO,MAAM,EAAE,iBAAa,CAAC;AAC7B,eAAO,MAAM,QAAQ,QAA2B,CAAC;AACjD,eAAO,MAAM,OAAO,UAAU,CAAC;AAE/B,KAAK,cAAc,GAAG;IACpB,OAAO,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE;QAAE,QAAQ,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IAC/C,MAAM,CAAC,EAAE;QAAE,KAAK,CAAC,EAAE,MAAM,EAAE,CAAA;KAAE,CAAC;CAC/B,CAAC;AA4BF,wBAAsB,MAAM;mBAET,cAAc;;GAqBhC;;;;;AAED,wBAA8B;AAE9B,OAAO,EAAE,OAAO,EAAE,YAAY,EAAE,aAAa,EAAE,UAAU,EAAE,CAAC;AAC5D,YAAY,EACV,SAAS,EACT,YAAY,EACZ,MAAM,EACN,QAAQ,EACR,QAAQ,EACR,aAAa,EACb,QAAQ,EACR,kBAAkB,EAClB,iBAAiB,EACjB,aAAa,GACd,MAAM,YAAY,CAAC"}

package/dist/index.js

@@ -1,9 +1,54 @@
-import { dirname, resolve } from "path";
+import { readFileSync } from "fs";
+import { dirname, join, relative, resolve, sep } from "path";
 import { fileURLToPath } from "url";
 import { VERSION, PACKAGE_NAME, PRODUCT_BRAND, SKILL_NAME, } from "./constants.js";
 const __dirname = dirname(fileURLToPath(import.meta.url));
 export const id = SKILL_NAME;
 export const repoRoot = resolve(__dirname, "..");
 export const version = VERSION;
+function commandNameForPath(filePath) {
+    const relativePath = relative(join(repoRoot, "commands"), filePath);
+    return relativePath.replace(/\.md$/, "").split(sep).join(":");
+}
+function pathForTemplate(filePath) {
+    return filePath.split(sep).join("/");
+}
+function anchorTrustedSkillReferences(template) {
+    const trustedSkillBundlePath = pathForTemplate(join(repoRoot, "skills", SKILL_NAME));
+    return template.replaceAll(`skills/${SKILL_NAME}/`, `${trustedSkillBundlePath}/`);
+}
+const commandFiles = [
+    "commands/autoresearch.md",
+    "commands/autoresearch/plan.md",
+    "commands/autoresearch/debug.md",
+    "commands/autoresearch/fix.md",
+    "commands/autoresearch/learn.md",
+    "commands/autoresearch/predict.md",
+    "commands/autoresearch/scenario.md",
+    "commands/autoresearch/security.md",
+    "commands/autoresearch/ship.md",
+];
+export async function server() {
+    return {
+        config(config) {
+            config.command = config.command || {};
+            config.skills = config.skills || {};
+            config.skills.paths = config.skills.paths || [];
+            if (!config.skills.paths.includes(repoRoot)) {
+                config.skills.paths.push(repoRoot);
+            }
+            for (const commandFile of commandFiles) {
+                const filePath = join(repoRoot, commandFile);
+                config.command[commandNameForPath(filePath)] ??= {
+                    template: anchorTrustedSkillReferences(readFileSync(filePath, "utf8").trim()),
+                };
+            }
+        },
+        event() {
+            return undefined;
+        },
+    };
+}
+export default { id, server };
 export { VERSION, PACKAGE_NAME, PRODUCT_BRAND, SKILL_NAME };
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
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package/dist/wizard.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"wizard.d.ts","sourceRoot":"","sources":["../src/wizard.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,YAAY,CAAC;AAY/C,wBAAgB,iBAAiB,CAC/B,IAAI,EAAE,MAAM,GAAG,SAAS,EACxB,MAAM,EAAE,YAAY,GACnB,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAkDzB"}

package/dist/wizard.js

@@ -2,7 +2,8 @@ import { basename } from "path";
 import { resolveRepo, normalizeDirection, normalizeMode, parseDurationSeconds, normalizeLabels, inferVerifyCommand, } from "./helpers.js";
 import { buildSubagentPoolPlan, buildContinuationPolicy } from "./subagent-pool.js";
 export function buildSetupSummary(repo, config) {
-    const verify = config.verify ?? inferVerifyCommand(repo);
+    const explicitVerify = config.verify?.trim();
+    const verify = explicitVerify || inferVerifyCommand(repo);
     const direction = normalizeDirection(config.direction);
     const mode = normalizeMode(config.mode);
     const durationSeconds = parseDurationSeconds(config.duration);
@@ -16,7 +17,7 @@ export function buildSetupSummary(repo, config) {
     const missingRequired = [];
     if (!config.goal)
         missingRequired.push("goal");
-    if (verify === "<set verify command>")
+    if (!explicitVerify)
         missingRequired.push("verify");
     const stopReasons = [];
     if (verify !== "<set verify command>") {
@@ -29,7 +30,7 @@ export function buildSetupSummary(repo, config) {
     const questions = [];
     if (!config.goal)
         questions.push({ id: "goal", prompt: "What outcome should this run optimize for?", reason: "The loop needs one concrete result to chase." });
-    if (!config.verify)
+    if (!explicitVerify)
         questions.push({ id: "verify", prompt: "What command should mechanically verify the metric?", reason: "The loop should not keep changes on intuition alone." });
     if (!config.mode)
         questions.push({ id: "mode", prompt: "Should the run stay in `foreground` or move to `background`?", reason: "The skill requires an explicit run-mode choice." });

package/dist/wizard.js.map

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package/docs/ARCHITECTURE.md

@@ -1,8 +1,17 @@
 # Auto Research Architecture
 
-> Current reference for v3.3.0.
+> Current reference for v3.3.3.
 
-Auto Research is an OpenCode-only npm package with recursive self-improvement capabilities. The runtime is Node.js ESM. All workflow semantics are preserved from earlier releases.
+Auto Research is a multi-runtime npm package with recursive self-improvement capabilities. The runtime is Node.js ESM. All workflow semantics are preserved from earlier releases.
+
+## Supported Runtimes
+
+| Runtime | Entry | Subagent Model | Background Mode |
+|---------|-------|----------------|-----------------|
+| OpenCode | `/autoresearch` slash commands | Standing pool (unlimited) | `autoresearch launch` |
+| Hermes Agent | Cronjob + `delegate_task` | Batch pool (max 3) | Native cron |
+
+Both runtimes share the same state format, CLI, and artifact paths.
 
 ## Package Layout
 
@@ -19,15 +28,22 @@ commands/autoresearch.md        # Main command
 commands/autoresearch/*.md     # Mode commands (plan, debug, fix, learn, etc.)
 skills/autoresearch/           # OpenCode skill bundle
 skills/autoresearch/references/# Workflow and runtime references
+skills/hermes/                 # Hermes Agent skill bundle
+  README.md                    # Hermes setup and usage
+  INTEGRATION.md               # Architecture and command mapping
+  autoresearch-prompt.md       # Cron prompt template
 hooks/init.sh                  # SessionStart hook
 hooks/status.sh                # Status hook
 hooks/stop.sh                  # Stop hook
 hooks/verify-package.sh        # Package verification
+INSTALL.md                     # Public raw install handoff (both runtimes)
+.opencode/INSTALL.md          # OpenCode native plugin install guide
 docs/OPENCODE_INSTALL.md       # OpenCode install guide
 docs/ARCHITECTURE.md           # This document
 docs/RELEASE.md                # Release process
 plugins/autoresearch.ts        # OpenCode plugin entry point
 .opencode-plugin/plugin.json   # OpenCode plugin manifest
+AGENTS.md                      # Repository-specific agent guide
 .autoresearch/                 # Runtime state directory (created at runtime)
 ```
 
@@ -36,15 +52,16 @@ plugins/autoresearch.ts        # OpenCode plugin entry point
 ```mermaid
 flowchart LR
     A[OpenCode /autoresearch] --> B[CLI]
+    H[Hermes Cronjob] --> B
     B --> C[Run Manager]
     C --> D[State JSON]
     C --> E[Results TSV]
     C --> F[Subagent Pool]
     F --> G[Orchestrator]
-    F --> H[Scout]
-    F --> I[Analyst]
-    F --> J[Verifier]
-    F --> K[Synthesizer]
+    F --> I[Scout]
+    F --> J[Analyst]
+    F --> K[Verifier]
+    F --> L[Synthesizer]
 ```
 
 ## Core Loop
@@ -52,7 +69,7 @@ flowchart LR
 ```mermaid
 flowchart TD
     A[Goal + Metric + Verify] --> B[Baseline]
-    B --> C[Standing Pool Init]
+    B --> C[Pool Init]
     C --> D[Iteration N]
     D --> E[Subagent Context]
     E --> F[Focused Change]
@@ -85,7 +102,7 @@ flowchart TD
 
 ## Source of Truth
 
-`src/` is authoritative for runtime behavior. `commands/` and `skills/` define the OpenCode surfaces.
+`src/` is authoritative for runtime behavior. `commands/` and `skills/autoresearch/` define the OpenCode surfaces. `skills/hermes/` defines the Hermes Agent surface.
 
 ## Runtime Artifacts
 
@@ -100,6 +117,8 @@ flowchart TD
 
 ## Command Surface
 
+### OpenCode
+
 | Command | Workflow |
 | --- | --- |
 | `/autoresearch` | Default improve-verify loop |
@@ -112,6 +131,21 @@ flowchart TD
 | `/autoresearch:security` | Security review |
 | `/autoresearch:ship` | Ship-readiness workflow |
 
+### Hermes
+
+| OpenCode Command | Hermes Equivalent |
+|-----------------|-------------------|
+| `/autoresearch` | Cron runs iteration loop |
+| `/autoresearch:plan` | Subagent task: plan experiments |
+| `/autoresearch:debug` | Subagent task: debug failures |
+| `/autoresearch:fix` | Subagent task: fix issues |
+| `/autoresearch:learn` | Memory tool + pattern analysis |
+| `autoresearch init` | Manual setup (same CLI) |
+| `autoresearch status` | `cat .autoresearch/state.json` |
+| `autoresearch launch` | `hermes cron create` |
+| `autoresearch stop` | `hermes cron pause` |
+| `autoresearch resume` | `hermes cron resume` |
+
 ## CLI Commands
 
 | Command | Purpose |
@@ -158,6 +192,15 @@ The standing pool provides:
 | `research_tracker` | Pattern tracking across iterations |
 | `meta_orchestrator` | Owns meta-goal and child loop decisions (self-improvement) |
 
+### Runtime Differences
+
+| Feature | OpenCode | Hermes |
+|---------|----------|--------|
+| Pool type | Standing (persistent across iterations) | Batch (spawned per phase) |
+| Max concurrent | Unlimited | 3 (Hermes limit) |
+| Real-time | Yes | 15-minute cron intervals |
+| Memory | File-based | `memory` tool + file |
+
 ## Validation
 
 1. `npm run typecheck` — TypeScript strict checks.
@@ -191,5 +234,6 @@ The release workflow is automated via GitHub Actions:
 - State is now in `.autoresearch/state.json` (was `autoresearch-state.json` at root).
 - Runtime helpers are TypeScript (`src/helpers.ts`) not Python.
 - Plugin format is `.opencode-plugin/plugin.json`.
-- The Claude and Codex plugin bundles (`plugins/autoresearch/`, `plugins/codex-autoresearch/`) are no longer shipped.
+- Legacy plugin bundles are no longer shipped.
 - Self-improvement loop added in v3.2.0.
+- Hermes Agent support added in v3.3.3.

package/docs/OPENCODE_INSTALL.md

@@ -1,48 +1,109 @@
 # OpenCode Install
 
-Install `opencode-autoresearch` as a global npm package.
+For the public raw install handoff, see [`../INSTALL.md`](../INSTALL.md).
 
-## Install
+## Recommended: OpenCode Plugin Install
 
-```bash
-npm install -g opencode-autoresearch
+Add Auto Research to the `plugin` array in your global or project-level `opencode.json`:
+
+```json
+{
+  "plugin": ["opencode-autoresearch@latest"]
+}
 ```
 
+Restart OpenCode. OpenCode installs npm plugins automatically at startup.
+
 ## Verify Installation
 
+Start the setup wizard inside OpenCode:
+
+```text
+/autoresearch
+```
+
+## Optional: Global CLI Install
+
 ```bash
+npm install -g opencode-autoresearch
 opencode-autoresearch doctor
 ```
 
-Should print the package version and confirm the plugin surfaces are in place.
+For one-time CLI use:
+
+```bash
+npx opencode-autoresearch doctor
+```
 
-## OpenCode Plugin Registration
+## OpenCode Commands
 
-After install, the plugin is available as `autoresearch`:
+| Command | Purpose |
+| --- | --- |
+| `/autoresearch` | Run the main improve-verify loop |
+| `/autoresearch:plan` | Planning workflow |
+| `/autoresearch:debug` | Debugging workflow |
+| `/autoresearch:fix` | Fix workflow |
+| `/autoresearch:learn` | Learning workflow |
+| `/autoresearch:predict` | Prediction workflow |
+| `/autoresearch:scenario` | Scenario expansion |
+| `/autoresearch:security` | Security review |
+| `/autoresearch:ship` | Ship-readiness workflow |
 
-- `/autoresearch` — Run the main improve-verify loop
-- `/autoresearch:plan` — Planning workflow
-- `/autoresearch:debug` — Debugging workflow
-- `/autoresearch:fix` — Fix workflow
-- `/autoresearch:learn` — Learning workflow
-- `/autoresearch:predict` — Prediction workflow
-- `/autoresearch:scenario` — Scenario expansion
-- `/autoresearch:security` — Security review
-- `/autoresearch:ship` — Ship-readiness workflow
+## Hermes Agent Commands
+
+Hermes uses cronjobs and `delegate_task` instead of slash commands. See [`../skills/hermes/INTEGRATION.md`](../skills/hermes/INTEGRATION.md) for the full command mapping.
+
+| OpenCode Command | Hermes Equivalent |
+|-----------------|-------------------|
+| `/autoresearch` | Cron runs iteration loop |
+| `/autoresearch:plan` | Subagent task: plan experiments |
+| `/autoresearch:debug` | Subagent task: debug failures |
+| `/autoresearch:fix` | Subagent task: fix issues |
+| `/autoresearch:learn` | Memory tool + pattern analysis |
+| `autoresearch init` | Manual setup (same CLI) |
+| `autoresearch status` | `cat .autoresearch/state.json` |
+| `autoresearch launch` | `hermes cron create` |
+| `autoresearch stop` | `hermes cron pause` |
+| `autoresearch resume` | `hermes cron resume` |
 
 ## Runtime Artifacts
 
-After install, artifacts are stored in `.autoresearch/` under the working directory:
+Artifacts are stored under the working directory:
 
 | Artifact | Purpose |
 | --- | --- |
 | `.autoresearch/state.json` | Current run state |
+| `.autoresearch/launch.json` | Background launch manifest |
 | `autoresearch-results.tsv` | Iteration log |
 | `autoresearch-report.md` | End-of-run report |
 | `autoresearch-memory.md` | Reusable memory |
 
-## Uninstall
+## Updating
+
+The `opencode-autoresearch@latest` plugin entry follows the current npm `latest` release. Restart OpenCode after a new Auto Research package release is available. To pin a fixed version instead:
+
+```json
+{
+  "plugin": ["opencode-autoresearch@3.3.4"]
+}
+```
+
+## Troubleshooting
+
+### Plugin not loading
+
+1. Verify `opencode.json` uses `"plugin": ["opencode-autoresearch@latest"]`.
+2. Restart OpenCode after editing config.
+3. Check logs with `opencode run --print-logs "hello"`.
+
+### CLI not found
+
+1. Run `npm install -g opencode-autoresearch`.
+2. Verify your npm global bin directory is on `PATH`.
+3. Run `opencode-autoresearch doctor`.
+
+## Uninstall CLI
 
 ```bash
 npm uninstall -g opencode-autoresearch
-```
+```

package/docs/QUICKSTART.md

@@ -2,11 +2,33 @@
 
 ## Installation
 
+### OpenCode
+
 ```bash
 npm install -g opencode-autoresearch
 autoresearch doctor
 ```
 
+### Hermes Agent
+
+```bash
+# 1. Install the skill
+git clone https://github.com/Maleick/AutoResearch.git
+cd AutoResearch
+npm install
+mkdir -p ~/.hermes/skills/software-development/autoresearch
+cp skills/hermes/autoresearch-prompt.md ~/.hermes/skills/software-development/autoresearch/SKILL.md
+cp skills/hermes/INTEGRATION.md ~/.hermes/skills/software-development/autoresearch/REFERENCES.md
+
+# 2. Create a cronjob
+hermes cron create \
+  --name "autoresearch-loop" \
+  --workdir ~/projects/AutoResearch \
+  --skill autoresearch-hermes \
+  "every 15m" \
+  "Run AutoResearch iteration loop. Detect phase from .autoresearch/state.json and execute one phase. Approved verify command: 'npm run test:coverage'. Approved guard command: 'npm run typecheck'."
+```
+
 ## Basic Usage
 
 ### 1. Initialize a run
@@ -66,6 +88,26 @@ autoresearch launch
 autoresearch status
 ```
 
+### Hermes Background Runs
+
+```bash
+# Initialize state from a trusted shell before enabling unattended cron
+autoresearch init \
+  --goal "Improve test coverage" \
+  --metric "coverage_pct" \
+  --direction "higher" \
+  --verify "npm run test:coverage" \
+  --guard "npm run typecheck" \
+  --iterations 20 \
+  --mode background
+
+# Start cron
+hermes cron resume autoresearch-loop
+
+# Check progress
+cat .autoresearch/state.json | jq .
+```
+
 ## Self-Improvement
 
 Run AutoResearch on itself:

package/docs/RELEASE.md

@@ -4,7 +4,7 @@ This package uses npm publish for releases. GitHub Actions automates the full re
 
 ## Version Alignment
 
-`VERSION`, `package.json`, `src/constants.ts`, and `.opencode-plugin/plugin.json` must all stay aligned. The `VERSION` file is the canonical source of truth.
+`VERSION`, `package.json`, `package-lock.json`, `src/constants.ts`, and `.opencode-plugin/plugin.json` must all stay aligned. The `VERSION` file is the canonical source of truth.
 
 ## Release Steps
 
@@ -12,10 +12,10 @@ This package uses npm publish for releases. GitHub Actions automates the full re
 
 ```bash
 # Update VERSION file
-echo "3.2.0" > VERSION
+echo "3.3.3" > VERSION
 
 # Sync to package.json
-npm version 3.2.0 --no-git-tag-version
+npm version 3.3.3 --no-git-tag-version
 
 # Sync to src/constants.ts
 # Update the VERSION export manually or use sed
@@ -36,25 +36,24 @@ npm test
 Add a new section for the version in `CHANGELOG.md`:
 
 ```markdown
-## [3.2.0] - YYYY-MM-DD
+## [3.3.3] - YYYY-MM-DD
 
 ### Added
-- Recursive self-improvement loop support
-- Mermaid diagrams in documentation
-- Enhanced subagent pool with meta-orchestrator role
+- Root install handoff
+- Public install verification notes
 
 ### Changed
-- Updated README with banner and visual diagrams
-- Improved wiki pages with architecture charts
+- Installation docs
+- Package verification allowlist
 ```
 
 ### 4. Commit and tag
 
 ```bash
 git add -A
-git commit -m "Release v3.2.0"
-git tag v3.2.0
-git push origin main v3.2.0
+git commit -m "Release v3.3.3"
+git tag v3.3.3
+git push origin main v3.3.3
 ```
 
 ### 5. Automated release
@@ -64,8 +63,8 @@ GitHub Actions will:
 1. Build and type-check
 2. Verify package contents
 3. Run tests
-4. Create a GitHub Release with CHANGELOG section
-5. Publish to npm
+4. Create a GitHub Release with the CHANGELOG section
+5. Publish to npm with provenance through trusted publishing
 
 ## Manual publish (fallback)
 
@@ -86,7 +85,9 @@ The shipped package includes:
 - `commands/` — OpenCode command surfaces (`autoresearch.md`, `autoresearch/*.md`)
 - `skills/autoresearch/` — Skill bundle with references
 - `hooks/` — Shell hooks for session lifecycle
-- `docs/` — Installation, architecture, and release docs
+- selected `docs/` files — `ARCHITECTURE.md`, `OPENCODE_INSTALL.md`, `QUICKSTART.md`, `RELEASE.md`, documentation site assets, and `CNAME`
+- `INSTALL.md` — Public raw OpenCode install handoff
+- `.opencode/INSTALL.md` — OpenCode native plugin install guide
 - `.opencode-plugin/plugin.json` — OpenCode plugin manifest
 - `AGENTS.md` — Agent guide
 - `VERSION` — Version marker

package/hooks/status.sh

@@ -7,18 +7,20 @@ set -e
 STATUS_FILE="${AUTORESEARCH_STATE:-.autoresearch/state.json}"
 
 if [ -f "$STATUS_FILE" ]; then
-  node --input-type=module -e "
-    import { readFileSync } from 'fs';
-    const s = JSON.parse(readFileSync('$STATUS_FILE', 'utf8'));
-    console.log('Auto Research run: ' + s.run_id);
-    console.log('Status: ' + s.status);
-    console.log('Mode: ' + s.mode);
-    console.log('Goal: ' + s.goal);
-    console.log('Iterations: ' + s.stats.total_iterations);
-    console.log('Kept: ' + s.stats.kept + ' | Discarded: ' + s.stats.discarded);
-    if (s.flags.needs_human) console.log('NEEDS HUMAN');
-    if (s.flags.stop_requested) console.log('STOP REQUESTED');
-  " 2>/dev/null || echo "No active run."
+  AUTORESEARCH_STATUS_FILE="$STATUS_FILE" node --input-type=module -e '
+    import { readFileSync } from "fs";
+    const statusFile = process.env.AUTORESEARCH_STATUS_FILE;
+    if (!statusFile) throw new Error("Missing AUTORESEARCH_STATUS_FILE");
+    const s = JSON.parse(readFileSync(statusFile, "utf8"));
+    console.log("Auto Research run: " + s.run_id);
+    console.log("Status: " + s.status);
+    console.log("Mode: " + s.mode);
+    console.log("Goal: " + s.goal);
+    console.log("Iterations: " + s.stats.total_iterations);
+    console.log("Kept: " + s.stats.kept + " | Discarded: " + s.stats.discarded);
+    if (s.flags.needs_human) console.log("NEEDS HUMAN");
+    if (s.flags.stop_requested) console.log("STOP REQUESTED");
+  ' 2>/dev/null || echo "No active run."
 else
   echo "No active run."
 fi

package/hooks/stop.sh

@@ -5,24 +5,58 @@
 set -e
 
 STATUS_FILE="${AUTORESEARCH_STATE:-.autoresearch/state.json}"
+WORKSPACE_ROOT="$(pwd -P)"
 
-if [ -f "$STATUS_FILE" ]; then
-  mode=$(node --input-type=module -e "
-    import { readFileSync } from 'fs';
-    const s = JSON.parse(readFileSync('$STATUS_FILE', 'utf8'));
-    console.log(s.mode || '');
-  " 2>/dev/null || true)
+case "$STATUS_FILE" in
+  /*) STATUS_FILE_ABS="$STATUS_FILE" ;;
+  *) STATUS_FILE_ABS="$WORKSPACE_ROOT/$STATUS_FILE" ;;
+esac
+
+if [ -L "$STATUS_FILE_ABS" ]; then
+  echo "Refusing symlinked state file."
+  exit 0
+fi
+
+STATUS_DIR="${STATUS_FILE_ABS%/*}"
+STATUS_NAME="${STATUS_FILE_ABS##*/}"
+STATUS_DIR_REAL="$(cd "$STATUS_DIR" 2>/dev/null && pwd -P)" || {
+  echo "No active run."
+  exit 0
+}
+STATUS_FILE_REAL="$STATUS_DIR_REAL/$STATUS_NAME"
+WORKSPACE_STATE_DIR="$WORKSPACE_ROOT/.autoresearch"
+
+case "$STATUS_FILE_REAL" in
+  "$WORKSPACE_STATE_DIR"/*) ;;
+  *)
+    echo "Refusing state file outside workspace."
+    exit 0
+    ;;
+esac
+
+if [ -f "$STATUS_FILE_ABS" ]; then
+  mode=$(AUTORESEARCH_STATUS_FILE="$STATUS_FILE_ABS" node --input-type=module -e '
+    import { readFileSync } from "fs";
+    const statusFile = process.env.AUTORESEARCH_STATUS_FILE;
+    if (!statusFile) throw new Error("Missing AUTORESEARCH_STATUS_FILE");
+    const s = JSON.parse(readFileSync(statusFile, "utf8"));
+    console.log(s.mode || "");
+  ' 2>/dev/null || true)
   if [ "$mode" = "background" ]; then
-    node --input-type=module -e "
-      import { readFileSync, writeFileSync } from 'fs';
-      const s = JSON.parse(readFileSync('$STATUS_FILE', 'utf8'));
+    AUTORESEARCH_STATUS_FILE="$STATUS_FILE_ABS" node --input-type=module -e '
+      import { readFileSync, renameSync, writeFileSync } from "fs";
+      const statusFile = process.env.AUTORESEARCH_STATUS_FILE;
+      if (!statusFile) throw new Error("Missing AUTORESEARCH_STATUS_FILE");
+      const s = JSON.parse(readFileSync(statusFile, "utf8"));
       s.updated_at = new Date().toISOString();
       s.flags.stop_requested = true;
       s.flags.background_active = false;
-      s.status = 'stopping';
-      writeFileSync('$STATUS_FILE', JSON.stringify(s, null, 2) + '\n');
-      console.log('Stop requested for run: ' + s.run_id);
-    " 2>/dev/null || echo "Could not update state."
+      s.status = "stopping";
+      const tmp = `${statusFile}.tmp.${process.pid}`;
+      writeFileSync(tmp, JSON.stringify(s, null, 2) + "\n", { mode: 0o600 });
+      renameSync(tmp, statusFile);
+      console.log("Stop requested for run: " + s.run_id);
+    ' 2>/dev/null || echo "Could not update state."
   else
     echo "Only background runs can be stopped."
   fi