@technomoron/agent-run 0.99.27 → 0.99.29

package/dist/project.js

@@ -164,6 +164,11 @@ function profileFromPackage(projectRoot) {
     if (fs.existsSync(packagePath)) {
         try {
             const pkg = JSON.parse(fs.readFileSync(packagePath, 'utf8'));
+            const repositoryProfile = parsePackageRepositoryProfile(pkg.repository);
+            if (repositoryProfile !== null) {
+                (0, utils_1.verbose)(`using package.json repository profile=${repositoryProfile}`);
+                return parseProfile(repositoryProfile, `${packagePath} repository`);
+            }
             if (typeof pkg.name === 'string' && pkg.name.length > 0) {
                 (0, utils_1.verbose)(`using package.json name=${pkg.name}`);
                 return parseProfile(pkg.name.startsWith('@') ? pkg.name.slice(1) : pkg.name, `${packagePath} name`);
@@ -183,6 +188,28 @@ function profileFromPackage(projectRoot) {
     }
     return { profile: null, reason: `cannot resolve agent profile from project path: ${projectRoot}` };
 }
+function parsePackageRepositoryProfile(repository) {
+    let repositoryPath = null;
+    if (typeof repository === 'string') {
+        repositoryPath = repository;
+    }
+    else if (repository !== null && typeof repository === 'object' && 'url' in repository) {
+        const url = repository.url;
+        if (typeof url === 'string') {
+            repositoryPath = url;
+        }
+    }
+    if (repositoryPath === null) {
+        return null;
+    }
+    const value = repositoryPath.trim();
+    const githubProfile = parseGitHubRemoteProfile(value.replace(/^git\+/, ''));
+    if (githubProfile !== null) {
+        return githubProfile;
+    }
+    const shorthand = /^(?:github:)?([^/:\s]+)\/([^/\s]+?)(?:\.git)?$/.exec(value);
+    return shorthand?.[1] && shorthand[2] ? `${shorthand[1]}/${shorthand[2]}` : null;
+}
 function resolveGitHubProfile(projectRoot) {
     const result = childProcess.spawnSync('git', ['-C', projectRoot, 'config', '--get', 'remote.origin.url'], {
         encoding: 'utf8',
@@ -271,17 +298,11 @@ function defaultConfigRoot(projectRoot, options = {}) {
     if (explicit !== null) {
         return explicit;
     }
-    if (projectRoot) {
-        const projectConfigRoot = defaultCodeConfigRoot(projectRoot);
-        if (options.preferProjectRoot || fs.existsSync(projectConfigRoot)) {
-            return projectConfigRoot;
-        }
-        return findExistingConfigRoot(defaultConfigRootSearchCandidates()) ?? projectConfigRoot;
-    }
-    return findExistingConfigRoot(defaultConfigRootSearchCandidates()) ?? path.join(os.homedir(), '.agent-config');
+    void options;
+    return path.join(os.homedir(), '.agent-run');
 }
 function explicitConfigRoot(projectRoot) {
-    for (const value of [process.env[constants_1.CONFIG_ROOT_OVERRIDE_ENV], process.env[constants_1.CONFIG_DIR_ENV], process.env.AGENT_CONFIG_ROOT]) {
+    for (const value of [process.env[constants_1.CONFIG_ROOT_OVERRIDE_ENV], process.env[constants_1.CONFIG_DIR_ENV]]) {
         if (value) {
             return path.resolve(value);
         }
@@ -290,21 +311,9 @@ function explicitConfigRoot(projectRoot) {
         return null;
     }
     const env = readAgentRunEnv(projectRoot);
-    const localValue = env[constants_1.CONFIG_DIR_ENV]?.trim() || env.AGENT_CONFIG_ROOT?.trim();
+    const localValue = env[constants_1.CONFIG_DIR_ENV]?.trim();
     return localValue ? path.resolve(projectRoot, localValue) : null;
 }
-function defaultCodeConfigRoot(projectRoot) {
-    const resolvedProjectRoot = path.resolve(projectRoot);
-    const ownerDir = path.dirname(resolvedProjectRoot);
-    const codeRoot = path.dirname(ownerDir);
-    if (ownerDir === resolvedProjectRoot || codeRoot === ownerDir) {
-        return path.join(os.homedir(), '.agent-config');
-    }
-    return path.join(codeRoot, 'agent-config');
-}
-function findExistingConfigRoot(candidates) {
-    return candidates.find((candidate) => fs.existsSync(candidate)) ?? null;
-}
 function defaultConfigRootSearchCandidates(_projectRoot, options = {}) {
     const platform = options.platform ?? process.platform;
     const pathApi = platform === 'win32' ? path.win32 : path.posix;

package/dist/renderer.js

@@ -51,11 +51,23 @@ function renderAgentSections(env, configRoot, manifest, context, trace) {
         }
         sections.push((0, templates_1.renderTemplateFile)(env, configRoot, include, context, trace));
     }
-    return sections.map((section, index) => {
+    const renderedSections = sections.map((section, index) => {
         const label = index === 0 ? manifest.agent.base : manifest.agent.includes[index - 1] ?? `section ${index}`;
         (0, templates_1.assertNoUnexpandedTemplateVars)(label, section);
         return section.trimEnd();
     });
+    renderedSections.push(projectMemoryInstructions(context));
+    return renderedSections;
+}
+function projectMemoryInstructions(context) {
+    return [
+        '## Project Memory',
+        '',
+        `Project memory is stored in ${context.paths.projectMemoryDir}.`,
+        'Read README.md there before starting work when prior project context may matter, then read only the linked files relevant to the task.',
+        'Do not store secrets, raw chat transcripts, or temporary task state there.',
+        'Update project memory only when the user explicitly asks you to remember or update something for this project.'
+    ].join('\n');
 }
 function renderProfileFiles(env, configRoot, context, targetTool, trace) {
     const files = [];
@@ -101,11 +113,18 @@ function syncAgentProfile(projectRoot, agentDir, options) {
 }
 function writeGeneratedFile(filePath, content, executable) {
     fs.mkdirSync(path.dirname(filePath), { recursive: true });
-    fs.writeFileSync(filePath, content, 'utf8');
+    const unchanged = fs.existsSync(filePath) && fs.readFileSync(filePath, 'utf8') === content;
+    if (!unchanged) {
+        fs.writeFileSync(filePath, content, 'utf8');
+        (0, utils_1.verbose)(`write ${filePath}`);
+    }
     if (executable && !constants_1.IS_WINDOWS) {
-        fs.chmodSync(filePath, 0o755);
+        const currentMode = fs.statSync(filePath).mode & 0o777;
+        if (currentMode !== 0o755) {
+            fs.chmodSync(filePath, 0o755);
+            (0, utils_1.verbose)(`chmod 755 ${filePath}`);
+        }
     }
-    (0, utils_1.verbose)(`write ${filePath}`);
 }
 function removeStaleGeneratedEntries(rendered) {
     const expectedFiles = new Set(rendered.files.map((file) => path.resolve(file.path)));
@@ -203,6 +222,7 @@ function checkRenderedFiles(rendered, findings) {
 function checkRuntimeDirectories(context, findings) {
     for (const dir of [
         context.paths.reviewDir,
+        context.paths.projectMemoryDir,
         context.paths.memoriesDir,
         context.paths.codexHomeDir,
         context.paths.liveDir,
@@ -296,6 +316,7 @@ function resolveProfileOverrideTemplate(configRoot, context, overrideFileName, g
 function syncRuntimeDirs(context) {
     for (const dir of [
         context.paths.reviewDir,
+        context.paths.projectMemoryDir,
         context.paths.memoriesDir,
         context.paths.codexHomeDir,
         context.paths.codexSkillsDir,
@@ -305,6 +326,11 @@ function syncRuntimeDirs(context) {
     ]) {
         fs.mkdirSync(dir, { recursive: true });
     }
+    const projectMemoryIndex = path.join(context.paths.projectMemoryDir, 'README.md');
+    if (!fs.existsSync(projectMemoryIndex)) {
+        fs.writeFileSync(projectMemoryIndex, (0, defaults_1.defaultProjectMemoryIndex)(), 'utf8');
+        (0, utils_1.verbose)(`created ${projectMemoryIndex}`);
+    }
     migrateLiveReviewFiles(context);
     removeLegacyCodexSkillDirs(context);
     removeLegacyCodeReviewSkillDirs(context);

package/dist/templates.js

@@ -35,6 +35,7 @@ function buildRenderContext(projectRoot, profileDir, configRoot, manifest, env)
     };
     const reviewDir = resolveRuntimePath(configRoot, manifest.paths.reviewDir, env, baseContext);
     const memoriesDir = resolveRuntimePath(configRoot, manifest.paths.memoriesDir, env, baseContext);
+    const projectMemoryDir = resolveRuntimePath(configRoot, manifest.paths.projectMemoryDir, env, baseContext);
     const codexHomeDir = path.join(memoriesDir, 'codex-home');
     const paths = {
         profileDir,
@@ -47,6 +48,8 @@ function buildRenderContext(projectRoot, profileDir, configRoot, manifest, env)
             : path.join(reviewDir, 'REVIEW.md'),
         memoriesDir,
         globalMemoryDir: path.join(configRoot, 'notes', 'memory'),
+        projectMemoryDir,
+        nativeMemoryDir: path.join(codexHomeDir, 'memories'),
         codexHomeDir,
         overridesDir: path.join(profileDir, 'overrides'),
         codexSkillsDir: path.join(codexHomeDir, 'skills'),

package/dist/tools.js

@@ -23,6 +23,7 @@ function runCodex(realBinary, permissionArgs, context, args, wrapperArgs) {
         AGENT_DIR: liveDir,
         AGENT_PROFILE_DIR: context.profileDir,
         AGENT_RUN_PROJECT_ROOT: projectRoot,
+        AGENT_PROJECT_MEMORY_DIR: context.paths.projectMemoryDir,
         AGENT_RUN_REAL_PATH: realPath,
         PATH: `${path.join(liveDir, 'bin')}${path.delimiter}${realPath}`
     };
@@ -30,6 +31,8 @@ function runCodex(realBinary, permissionArgs, context, args, wrapperArgs) {
     (0, process_1.execCommand)(realBinary, [
         ...permissionArgs,
         ...runtimeArgs,
+        '--add-dir',
+        context.paths.projectMemoryDir,
         '-C',
         projectRoot,
         ...(wrapperArgs.sandboxMode !== 'danger' && wrapperArgs.codexNetwork
@@ -51,12 +54,15 @@ function runClaude(realBinary, permissionArgs, context, args, wrapperArgs) {
         AGENT_DIR: liveDir,
         AGENT_PROFILE_DIR: context.profileDir,
         AGENT_RUN_PROJECT_ROOT: context.projectRoot,
+        AGENT_PROJECT_MEMORY_DIR: context.paths.projectMemoryDir,
         AGENT_RUN_REAL_PATH: realPath,
         PATH: `${path.join(liveDir, 'bin')}${path.delimiter}${realPath}`
     };
     const runtimeArgs = wrapperArgs.sandboxMode === 'danger' ? getDangerArgs('claude') : permissionArgs;
     (0, process_1.execCommand)(realBinary, [
         ...runtimeArgs,
+        '--add-dir',
+        context.paths.projectMemoryDir,
         '--append-system-prompt-file',
         claudePath,
         '--settings',

package/examples/basic-config/README.md

@@ -9,7 +9,8 @@ It contains two pieces:
   config root.
 - `agent-config/`: a complete config root with shared manifest defaults, global
   templates, snippets, skill templates, a personal memory skill, a sparse
-  profile manifest, profile-local instructions, and profile overrides.
+  profile manifest, durable project memory, profile-local instructions, and
+  profile overrides.
 
 Try it from this repository after building:
 

package/examples/basic-config/agent-config/agent-run.defaults.jsonc

@@ -33,6 +33,7 @@
     "changesFile": "{{ projectRoot }}/CHANGES",
     "reviewDir": "{{ profileDir }}/reviews",
     "reviewFile": "{{ profileDir }}/reviews/REVIEW-{{ date }}.md",
-    "memoriesDir": "{{ agentDir }}/memories"
+    "memoriesDir": "{{ agentDir }}/memories",
+    "projectMemoryDir": "{{ profileDir }}/notes/memory"
   }
 }

package/examples/basic-config/agent-config/global/tool-templates/AGENTS.md.njk

@@ -14,6 +14,8 @@ Do not edit this generated file. Edit root defaults or profile-specific source f
 - reviewFile: `{{ paths.reviewFile }}`
 - reviewConsolidatedFile: `{{ paths.reviewConsolidatedFile }}`
 - memoriesDir: `{{ paths.memoriesDir }}`
+- nativeMemoryDir: `{{ paths.nativeMemoryDir }}`
+- projectMemoryDir: `{{ paths.projectMemoryDir }}`
 - globalMemoryDir: `{{ paths.globalMemoryDir }}`
 
 ## Skills

package/examples/basic-config/agent-config/global/tool-templates/CLAUDE.md.njk

@@ -6,4 +6,5 @@
 {% endfor %}
 Claude reads this file from the private agent directory.
 
+projectMemoryDir: `{{ paths.projectMemoryDir }}`
 globalMemoryDir: `{{ paths.globalMemoryDir }}`

package/examples/basic-config/agent-config/global/tool-templates/claude-settings.json.njk

@@ -3,6 +3,7 @@
     "AGENT_DIR": {{ agentDir | dump }},
     "AGENT_PROFILE_DIR": {{ profileDir | dump }},
     "AGENT_RUN_PROJECT_ROOT": {{ projectRoot | dump }},
+    "AGENT_PROJECT_MEMORY_DIR": {{ paths.projectMemoryDir | dump }},
     "AGENT_GLOBAL_MEMORY_DIR": {{ paths.globalMemoryDir | dump }},
     "STARTER_PROFILE": {{ profile | dump }}
   },
@@ -15,6 +16,7 @@
     "AGENT_DIR": {{ agentDir | dump }},
     "AGENT_PROFILE_DIR": {{ profileDir | dump }},
     "AGENT_RUN_PROJECT_ROOT": {{ projectRoot | dump }},
+    "AGENT_PROJECT_MEMORY_DIR": {{ paths.projectMemoryDir | dump }},
     "AGENT_GLOBAL_MEMORY_DIR": {{ paths.globalMemoryDir | dump }},
     "STARTER_PROFILE": {{ profile | dump }}
   }

package/examples/basic-config/agent-config/global/tool-templates/codex-config.toml.njk

@@ -7,6 +7,7 @@ sandbox_mode = "workspace-write"
 writable_roots = [
   {{ projectRoot | dump }},
   {{ paths.reviewDir | dump }},
-  {{ paths.memoriesDir | dump }}
+  {{ paths.memoriesDir | dump }},
+  {{ paths.projectMemoryDir | dump }}
 ]
 network_access = false

package/examples/basic-config/agent-config/starter/basic-project/notes/memory/README.md

@@ -0,0 +1,8 @@
+# Project memory
+
+This directory contains durable notes for this project across agent sessions and machines.
+Keep the notes short, factual, and free of secrets. Link additional topic files from this index.
+
+## Files
+
+- Add project memory files here as they are needed.

package/examples/basic-config/agent-config/starter/basic-project/overrides/claude-settings.json.njk

@@ -3,6 +3,7 @@
     "AGENT_DIR": {{ agentDir | dump }},
     "AGENT_PROFILE_DIR": {{ profileDir | dump }},
     "AGENT_RUN_PROJECT_ROOT": {{ projectRoot | dump }},
+    "AGENT_PROJECT_MEMORY_DIR": {{ paths.projectMemoryDir | dump }},
     "AGENT_GLOBAL_MEMORY_DIR": {{ paths.globalMemoryDir | dump }},
     "STARTER_PROFILE": {{ profile | dump }},
     "STARTER_OVERRIDE": "true"
@@ -16,6 +17,7 @@
     "AGENT_DIR": {{ agentDir | dump }},
     "AGENT_PROFILE_DIR": {{ profileDir | dump }},
     "AGENT_RUN_PROJECT_ROOT": {{ projectRoot | dump }},
+    "AGENT_PROJECT_MEMORY_DIR": {{ paths.projectMemoryDir | dump }},
     "AGENT_GLOBAL_MEMORY_DIR": {{ paths.globalMemoryDir | dump }},
     "STARTER_PROFILE": {{ profile | dump }},
     "STARTER_OVERRIDE": "true"

package/examples/basic-config/agent-config/starter/basic-project/overrides/codex-config.toml.njk

@@ -7,6 +7,7 @@ sandbox_mode = "workspace-write"
 writable_roots = [
   {{ projectRoot | dump }},
   {{ paths.reviewDir | dump }},
-  {{ paths.memoriesDir | dump }}
+  {{ paths.memoriesDir | dump }},
+  {{ paths.projectMemoryDir | dump }}
 ]
 network_access = false

package/ops/systemd/ai-tools-update.service

@@ -13,4 +13,4 @@ Environment=XDG_CONFIG_HOME=/root/.config
 Environment=NPM_CONFIG_PREFIX=/usr/local
 Environment=PNPM_HOME=/usr/local
 Environment=PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
-ExecStart=/usr/local/lib/agent-run/update-ai-tools.sh
+ExecStart=/usr/local/libexec/agent-run/update-ai-tools

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@technomoron/agent-run",
-  "version": "0.99.27",
+  "version": "0.99.29",
   "packageManager": "pnpm@10.28.1",
   "bin": {
     "agent-run": "dist/agent-run.js"

package/scripts/install-systemd-jobs.sh

@@ -19,10 +19,20 @@ USAGE
 }
 
 ROOT="$(cd "$(dirname "$0")/.." && pwd)"
-INSTALL_LIB_DIR="${INSTALL_LIB_DIR:-/usr/local/lib/agent-run}"
+SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
+INSTALL_LIBEXEC_DIR="${INSTALL_LIBEXEC_DIR:-${INSTALL_LIB_DIR:-/usr/local/libexec/agent-run}}"
 SYSTEMD_DIR="${SYSTEMD_DIR:-/etc/systemd/system}"
 ORIGINAL_ARGS=("$@")
 
+UPDATE_SCRIPT="$ROOT/scripts/update-ai-tools.sh"
+SERVICE_FILE="$ROOT/ops/systemd/ai-tools-update.service"
+TIMER_FILE="$ROOT/ops/systemd/ai-tools-update.timer"
+if [ ! -f "$UPDATE_SCRIPT" ]; then
+	UPDATE_SCRIPT="$SCRIPT_DIR/update-ai-tools.sh"
+	SERVICE_FILE="$SCRIPT_DIR/ai-tools-update.service"
+	TIMER_FILE="$SCRIPT_DIR/ai-tools-update.timer"
+fi
+
 INSTALL_AI_TOOLS=0
 DRY_RUN=0
 
@@ -71,10 +81,10 @@ run() {
 	"$@"
 }
 
-run install -d -m 0755 "$INSTALL_LIB_DIR" "$SYSTEMD_DIR"
-run install -m 0755 "$ROOT/scripts/update-ai-tools.sh" "$INSTALL_LIB_DIR/update-ai-tools.sh"
-run install -m 0644 "$ROOT/ops/systemd/ai-tools-update.service" "$SYSTEMD_DIR/ai-tools-update.service"
-run install -m 0644 "$ROOT/ops/systemd/ai-tools-update.timer" "$SYSTEMD_DIR/ai-tools-update.timer"
+run install -d -m 0755 "$INSTALL_LIBEXEC_DIR" "$SYSTEMD_DIR"
+run install -m 0755 "$UPDATE_SCRIPT" "$INSTALL_LIBEXEC_DIR/update-ai-tools"
+run install -m 0644 "$SERVICE_FILE" "$SYSTEMD_DIR/ai-tools-update.service"
+run install -m 0644 "$TIMER_FILE" "$SYSTEMD_DIR/ai-tools-update.timer"
 
 if [ "$INSTALL_AI_TOOLS" -eq 1 ]; then
 	run systemctl daemon-reload

package/scripts/update-ai-tools.sh

@@ -6,18 +6,44 @@ export NPM_CONFIG_PREFIX="${NPM_CONFIG_PREFIX:-/usr/local}"
 export PNPM_HOME="${PNPM_HOME:-/usr/local}"
 export PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:${PATH:-}"
 
-NPM_BIN="${AI_TOOLS_NPM_BIN:-/usr/local/bin/npm}"
+NPM_BIN="${AI_TOOLS_NPM_BIN:-/usr/bin/npm}"
+NODE_BIN="${AI_TOOLS_NODE_BIN:-/usr/bin/node}"
 APT_GET_BIN="${AI_TOOLS_APT_GET_BIN:-/usr/bin/apt-get}"
 
 AI_TOOLS_NPM_PACKAGES="${AI_TOOLS_NPM_PACKAGES:-npm@latest pnpm@latest corepack@latest fallow@latest ripgrep@latest pm2@latest tsx@latest typescript@latest @openai/codex@latest @anthropic-ai/claude-code@latest @technomoron/agent-run@latest}"
 AI_TOOLS_PNPM_PACKAGE="${AI_TOOLS_PNPM_PACKAGE:-pnpm@latest}"
 AI_TOOLS_APT_PACKAGES="${AI_TOOLS_APT_PACKAGES:-gh}"
+AI_TOOLS_CLEAN_BINS="${AI_TOOLS_CLEAN_BINS:-agent-run claude codex}"
+AI_TOOLS_SYSTEM_BIN_DIRS="${AI_TOOLS_SYSTEM_BIN_DIRS:-/usr/local/bin /usr/bin}"
 
 if [ "$(id -u)" -ne 0 ]; then
 	echo "update-ai-tools.sh must run as root" >&2
 	exit 1
 fi
 
+clean_tool_bins() {
+	local bin_dir="$1"
+	local bin_name
+	local -a bin_names
+
+	[ -d "$bin_dir" ] || return 0
+	read -r -a bin_names <<<"$AI_TOOLS_CLEAN_BINS"
+	for bin_name in "${bin_names[@]}"; do
+		case "$bin_name" in
+			agent-run|claude|codex)
+				rm -f -- "$bin_dir/$bin_name"
+				;;
+			*)
+				echo "Refusing to clean unexpected AI tool bin: $bin_name" >&2
+				exit 1
+				;;
+		esac
+	done
+}
+
+target_bin_dir="${NPM_CONFIG_PREFIX%/}/bin"
+clean_tool_bins "$target_bin_dir"
+
 if [ -n "$AI_TOOLS_NPM_PACKAGES" ]; then
 	read -r -a npm_packages <<<"$AI_TOOLS_NPM_PACKAGES"
 	"$NPM_BIN" install -g --force "${npm_packages[@]}"
@@ -30,9 +56,18 @@ if [ -n "$AI_TOOLS_PNPM_PACKAGE" ]; then
 	"$NPM_BIN" install -g --force "${pnpm_packages[@]}"
 fi
 
+# Once the new launchers are installed, remove exact-name duplicates from the
+# other conventional system prefix so PATH ordering cannot select a stale copy.
+read -r -a system_bin_dirs <<<"$AI_TOOLS_SYSTEM_BIN_DIRS"
+for system_bin_dir in "${system_bin_dirs[@]}"; do
+	if [ "${system_bin_dir%/}" != "${target_bin_dir%/}" ]; then
+		clean_tool_bins "$system_bin_dir"
+	fi
+done
+
 CLAUDE_INSTALL="$("$NPM_BIN" root -g)/@anthropic-ai/claude-code/install.cjs"
 if [ -f "$CLAUDE_INSTALL" ]; then
-	/usr/local/bin/node "$CLAUDE_INSTALL"
+	"$NODE_BIN" "$CLAUDE_INSTALL"
 fi
 
 if [ -n "$AI_TOOLS_APT_PACKAGES" ] && command -v "$APT_GET_BIN" >/dev/null 2>&1; then