@phnx-labs/agents-cli 1.14.2 → 1.14.3

package/dist/lib/session/discover.js

@@ -1451,12 +1451,12 @@ function normalizeVersion(version) {
     const trimmed = version?.trim();
     return trimmed ? trimmed : undefined;
 }
-/** Extract the version number from a managed ~/.agents-system/versions/<agent>/<version>/... path. */
+/** Extract the version number from a managed ~/.agents/versions/<agent>/<version>/... path. */
 function extractVersionFromManagedPath(agent, sourcePath) {
     if (!sourcePath)
         return undefined;
     const candidates = [sourcePath, safeRealpathSync(sourcePath) || ''];
-    const marker = `/.agents-system/versions/${agent}/`;
+    const marker = `/.agents/versions/${agent}/`;
     for (const candidate of candidates) {
         if (!candidate)
             continue;

package/dist/lib/session/render.js

@@ -424,6 +424,7 @@ export function renderSummary(events, cwd) {
     // Plan items
     const todoItems = [];
     let exitPlanContent = null;
+    let planFilePath = null;
     // Subagent spawns
     const subagents = [];
     // Errors
@@ -444,8 +445,14 @@ export function renderSummary(events, cwd) {
                     filesReadAbs.add(p);
             }
             else if (['Write', 'Edit', 'write_file', 'edit_file', 'create_file', 'replace', 'patch'].includes(tool)) {
-                if (p)
-                    (isInsideCwd(p) || !cwd ? filesModifiedAbs : filesModifiedExternal).add(p);
+                if (p) {
+                    if (p.includes('.claude/plans/') && p.endsWith('.md')) {
+                        planFilePath = p;
+                    }
+                    else {
+                        (isInsideCwd(p) || !cwd ? filesModifiedAbs : filesModifiedExternal).add(p);
+                    }
+                }
             }
             if (event.command) {
                 const cmd = event.command.replace(/\n/g, ' ').trim();
@@ -543,14 +550,19 @@ export function renderSummary(events, cwd) {
     if (firstUserMessage || attachments.length > 0)
         lines.push('');
     // 2. Plan
-    if (todoItems.length > 0 || exitPlanContent) {
+    if (todoItems.length > 0 || exitPlanContent || planFilePath) {
         lines.push(chalk.bold('Plan'));
+        if (planFilePath) {
+            const home = process.env.HOME ?? '';
+            const displayPath = home && planFilePath.startsWith(home) ? planFilePath.replace(home, '~') : planFilePath;
+            lines.push('  ' + chalk.cyan(displayPath));
+        }
         if (exitPlanContent) {
             const planLines = exitPlanContent.split('\n').slice(0, 10);
             for (const l of planLines)
                 lines.push('  ' + l);
         }
-        else {
+        else if (todoItems.length > 0) {
             for (const item of todoItems.slice(0, 20)) {
                 lines.push('  · ' + item);
             }
@@ -574,12 +586,14 @@ export function renderSummary(events, cwd) {
         lines.push('');
     }
     // 4b. External edits (files edited outside the project root — typically /tmp)
-    if (filesModifiedExternal.size > 0) {
-        const externalList = [...filesModifiedExternal].sort();
+    // Filter out plan files (already shown in Plan section)
+    const externalNonPlan = [...filesModifiedExternal].filter(p => !(p.includes('.claude/plans/') && p.endsWith('.md')));
+    if (externalNonPlan.length > 0) {
+        const externalList = externalNonPlan.sort();
         const home = process.env.HOME ?? '';
         const display = externalList.slice(0, 3).map(p => home && p.startsWith(home) ? p.replace(home, '~') : p);
         const more = externalList.length > 3 ? chalk.gray(` +${externalList.length - 3} more`) : '';
-        lines.push(chalk.gray(`External edits (${filesModifiedExternal.size}): ${display.join(', ')}${more}`));
+        lines.push(chalk.gray(`External edits (${externalList.length}): ${display.join(', ')}${more}`));
         lines.push('');
     }
     // 5. Read files

package/dist/lib/shims.d.ts

@@ -42,9 +42,9 @@ export declare function promptConflictStrategy(conflictInfos: ConflictInfo[]): P
  *
  * History:
  *   v1 — initial shim (implicit, no marker).
- *   v2 — `--version=...` form in sync/refresh-memory calls; refresh-memory
+ *   v2 — `--version=...` form in sync/refresh-rules calls; refresh-rules
  *        shim hook for non-@-capable agents.
- *   v3 — sync/refresh-memory flag renamed `--version` → `--agent-version`
+ *   v3 — sync/refresh-rules flag renamed `--version` → `--agent-version`
  *        so it no longer collides with commander's top-level `--version`.
  *   v4 — project version marker changed from `.agents-version` to a
  *        root-level `agents.yaml`; shim now skips ~/.agents/agents.yaml
@@ -53,8 +53,12 @@ export declare function promptConflictStrategy(conflictInfos: ConflictInfo[]): P
  *        sandbox_mode, rules/agents-deny.rules) is actually read by the codex
  *        binary instead of $HOME/.codex.
  *   v6 — hard-disable Codex startup update checks in the generated shims.
+ *   v7 — rename `agents refresh-memory` invocation to `agents refresh-rules`
+ *        and capability flag `memoryImports` → `rulesImports`.
+ *   v8 — versions moved from ~/.agents-system/versions to ~/.agents/versions
+ *        (two-repo split: system = shipped defaults, user = operational state).
  */
-export declare const SHIM_SCHEMA_VERSION = 6;
+export declare const SHIM_SCHEMA_VERSION = 8;
 /**
  * Generate the full bash shim script for the given agent. The returned string
  * is written to ~/.agents/shims/{cliCommand} and made executable.
@@ -83,8 +87,10 @@ export declare function removeShim(agent: AgentId): boolean;
  *        read the versioned permissions/rules instead of $HOME/.codex.
  *   v4 — direct aliases read binaries and config homes from ~/.agents-system.
  *   v5 — hard-disable Codex startup update checks in versioned aliases.
+ *   v6 — versions moved from ~/.agents-system/versions to ~/.agents/versions
+ *        (two-repo split: system = shipped defaults, user = operational state).
  */
-export declare const VERSIONED_ALIAS_SCHEMA_VERSION = 5;
+export declare const VERSIONED_ALIAS_SCHEMA_VERSION = 6;
 /**
  * Generate a versioned alias script that directly execs a specific version.
  * e.g., claude@2.0.65 -> directly runs that version's binary
@@ -219,8 +225,26 @@ export declare function getShimPath(agent: AgentId): string;
 /**
  * Return the first executable path that would be launched for this agent when
  * resolving against PATH, excluding the managed shim itself.
+ *
+ * Legacy ~/.agents/shims/<cli> (from the pre-split single-root layout) is NOT
+ * treated as a shadow when a current managed shim exists at getShimPath() —
+ * that file is dead weight from the old layout and the repair flow removes it
+ * separately. Treating it as "shadowing" caused an infinite repair-prompt
+ * loop because addShimsToPath() only edits the rc file, never the legacy
+ * shim file itself.
  */
 export declare function getPathShadowingExecutable(agent: AgentId): string | null;
+/**
+ * Delete the legacy ~/.agents/shims/<cli> file if it exists, returning whether
+ * anything was removed. Pre-split installs put shims under ~/.agents/shims/;
+ * the new layout uses ~/.agents-system/shims/. The leftover file causes the
+ * repair-prompt loop reported in RUSH-664 — `getPathShadowingExecutable` flags
+ * it as a shadow but `addShimsToPath` only edits rc files, never the file
+ * itself. Removing it ends the loop.
+ */
+export declare function removeLegacyUserShim(agent: AgentId, overrides?: {
+    homeDir?: string;
+}): boolean;
 /**
  * Check if the agent's CLI command is shadowed by a shell alias.
  *

package/dist/lib/shims.js

@@ -156,9 +156,9 @@ export async function promptConflictStrategy(conflictInfos) {
  *
  * History:
  *   v1 — initial shim (implicit, no marker).
- *   v2 — `--version=...` form in sync/refresh-memory calls; refresh-memory
+ *   v2 — `--version=...` form in sync/refresh-rules calls; refresh-rules
  *        shim hook for non-@-capable agents.
- *   v3 — sync/refresh-memory flag renamed `--version` → `--agent-version`
+ *   v3 — sync/refresh-rules flag renamed `--version` → `--agent-version`
  *        so it no longer collides with commander's top-level `--version`.
  *   v4 — project version marker changed from `.agents-version` to a
  *        root-level `agents.yaml`; shim now skips ~/.agents/agents.yaml
@@ -167,8 +167,12 @@ export async function promptConflictStrategy(conflictInfos) {
  *        sandbox_mode, rules/agents-deny.rules) is actually read by the codex
  *        binary instead of $HOME/.codex.
  *   v6 — hard-disable Codex startup update checks in the generated shims.
+ *   v7 — rename `agents refresh-memory` invocation to `agents refresh-rules`
+ *        and capability flag `memoryImports` → `rulesImports`.
+ *   v8 — versions moved from ~/.agents-system/versions to ~/.agents/versions
+ *        (two-repo split: system = shipped defaults, user = operational state).
  */
-export const SHIM_SCHEMA_VERSION = 6;
+export const SHIM_SCHEMA_VERSION = 8;
 /** Internal marker string used to embed the schema version in shim scripts. */
 const SHIM_VERSION_MARKER = 'agents-shim-version:';
 /**
@@ -194,16 +198,16 @@ export CLAUDE_CONFIG_DIR="$VERSION_DIR/home/${configDirName}"
 export CODEX_HOME="$VERSION_DIR/home/${configDirName}"
 `
             : '';
-    // Agents that don't natively resolve @-imports in their memory file need
+    // Agents that don't natively resolve @-imports in their rules file need
     // agents-cli to recompile when the user edits a rule/preset file. The
     // check is fast (sha256 of ~8 small files) and skips the recompile when
     // sources haven't changed.
-    const refreshMemoryCall = !agentConfig.capabilities.memoryImports
+    const refreshRulesCall = !agentConfig.capabilities.rulesImports
         ? `
-# Recompile memory if any rule/preset source has changed since last sync.
+# Recompile rules if any rule/preset source has changed since last sync.
 # Fast-path check (~10-20ms) when nothing changed; full recompile only on
 # actual diff. Non-blocking failure — if the refresh errors, we still launch.
-agents refresh-memory --agent "$AGENT" --agent-version "$VERSION" --quiet 2>/dev/null || true
+agents refresh-rules --agent "$AGENT" --agent-version "$VERSION" --quiet 2>/dev/null || true
 `
         : '';
     const launchArgs = agent === 'codex' ? ' -c check_for_update_on_startup=false' : '';
@@ -283,7 +287,7 @@ if [ -z "$VERSION" ]; then
   exit 1
 fi
 
-VERSION_DIR="$AGENTS_SYSTEM_DIR/versions/$AGENT/$VERSION"
+VERSION_DIR="$AGENTS_USER_DIR/versions/$AGENT/$VERSION"
 BINARY="$VERSION_DIR/node_modules/.bin/$CLI_COMMAND"
 
 # Auto-install if not present
@@ -328,7 +332,7 @@ PROJECT_AGENTS_DIR=$(find_project_agents_dir)
 if [ -n "$PROJECT_AGENTS_DIR" ]; then
   agents sync --agent "$AGENT" --agent-version "$VERSION" --project-dir "$PROJECT_AGENTS_DIR" --quiet >/dev/null 2>&1
 fi
-${refreshMemoryCall}${managedEnv}
+${refreshRulesCall}${managedEnv}
 
 exec "$BINARY"${launchArgs} "$@"
 `;
@@ -373,8 +377,10 @@ export function removeShim(agent) {
  *        read the versioned permissions/rules instead of $HOME/.codex.
  *   v4 — direct aliases read binaries and config homes from ~/.agents-system.
  *   v5 — hard-disable Codex startup update checks in versioned aliases.
+ *   v6 — versions moved from ~/.agents-system/versions to ~/.agents/versions
+ *        (two-repo split: system = shipped defaults, user = operational state).
  */
-export const VERSIONED_ALIAS_SCHEMA_VERSION = 5;
+export const VERSIONED_ALIAS_SCHEMA_VERSION = 6;
 /** Internal marker string used to embed the schema version in versioned alias scripts. */
 const VERSIONED_ALIAS_VERSION_MARKER = 'agents-versioned-alias-version:';
 // The version string is interpolated into a generated bash script and into
@@ -399,14 +405,14 @@ export function generateVersionedAliasScript(agent, version) {
         ? `
 # Claude stores OAuth credentials in the macOS keychain. Scope them to this
 # version's config directory so direct aliases also switch the live account.
-export CLAUDE_CONFIG_DIR="$HOME/.agents-system/versions/${agent}/${version}/home/${configDirName}"
+export CLAUDE_CONFIG_DIR="$HOME/.agents/versions/${agent}/${version}/home/${configDirName}"
 `
         : agent === 'codex'
             ? `
 # Codex reads its config (approval_policy, sandbox_mode, MCP servers, rules)
 # from CODEX_HOME. Point direct aliases at the versioned home so permissions
 # and rules written by agents-cli actually take effect.
-export CODEX_HOME="$HOME/.agents-system/versions/${agent}/${version}/home/${configDirName}"
+export CODEX_HOME="$HOME/.agents/versions/${agent}/${version}/home/${configDirName}"
 `
             : '';
     const launchArgs = agent === 'codex' ? ' -c check_for_update_on_startup=false' : '';
@@ -415,7 +421,7 @@ export CODEX_HOME="$HOME/.agents-system/versions/${agent}/${version}/home/${conf
 # ${VERSIONED_ALIAS_VERSION_MARKER} ${VERSIONED_ALIAS_SCHEMA_VERSION}
 # Direct alias for ${agentConfig.name}@${version}
 
-BINARY="$HOME/.agents-system/versions/${agent}/${version}/node_modules/.bin/${agentConfig.cliCommand}"
+BINARY="$HOME/.agents/versions/${agent}/${version}/node_modules/.bin/${agentConfig.cliCommand}"
 
 if [ ! -x "$BINARY" ]; then
   echo "agents: ${agent}@${version} not installed" >&2
@@ -1021,20 +1027,72 @@ export function getShimPath(agent) {
 /**
  * Return the first executable path that would be launched for this agent when
  * resolving against PATH, excluding the managed shim itself.
+ *
+ * Legacy ~/.agents/shims/<cli> (from the pre-split single-root layout) is NOT
+ * treated as a shadow when a current managed shim exists at getShimPath() —
+ * that file is dead weight from the old layout and the repair flow removes it
+ * separately. Treating it as "shadowing" caused an infinite repair-prompt
+ * loop because addShimsToPath() only edits the rc file, never the legacy
+ * shim file itself.
  */
 export function getPathShadowingExecutable(agent) {
     const pathDirs = (process.env.PATH || '').split(path.delimiter).filter(Boolean);
     const shimPath = path.resolve(getShimPath(agent));
     const cliCommand = AGENTS[agent].cliCommand;
+    const legacyUserShim = path.resolve(path.join(os.homedir(), '.agents', 'shims', cliCommand));
+    const managedShimExists = fs.existsSync(shimPath);
     for (const dir of pathDirs) {
         const candidate = path.resolve(dir, cliCommand);
         if (!fs.existsSync(candidate)) {
             continue;
         }
-        return candidate === shimPath ? null : candidate;
+        if (candidate === shimPath)
+            return null;
+        if (candidate === legacyUserShim && managedShimExists) {
+            // Legacy file from the pre-split layout. Don't treat as shadow — the
+            // repair flow deletes it via removeLegacyUserShim instead. Continue
+            // scanning so a real binary later in PATH is still detected.
+            continue;
+        }
+        return candidate;
     }
     return null;
 }
+/**
+ * Delete the legacy ~/.agents/shims/<cli> file if it exists, returning whether
+ * anything was removed. Pre-split installs put shims under ~/.agents/shims/;
+ * the new layout uses ~/.agents-system/shims/. The leftover file causes the
+ * repair-prompt loop reported in RUSH-664 — `getPathShadowingExecutable` flags
+ * it as a shadow but `addShimsToPath` only edits rc files, never the file
+ * itself. Removing it ends the loop.
+ */
+export function removeLegacyUserShim(agent, overrides) {
+    const cliCommand = AGENTS[agent].cliCommand;
+    const homeDir = overrides?.homeDir || os.homedir();
+    const legacyPath = path.join(homeDir, '.agents', 'shims', cliCommand);
+    if (!fs.existsSync(legacyPath))
+        return false;
+    // Belt-and-suspenders: only remove if the current managed shim location is
+    // different (it always should be — getShimsDir() returns the system dir —
+    // but guard against future refactors that might collapse the two).
+    const currentShim = path.resolve(getShimPath(agent));
+    if (path.resolve(legacyPath) === currentShim)
+        return false;
+    try {
+        fs.unlinkSync(legacyPath);
+        // Best-effort: clean up the legacy shims dir if empty.
+        try {
+            const legacyDir = path.dirname(legacyPath);
+            if (fs.readdirSync(legacyDir).length === 0)
+                fs.rmdirSync(legacyDir);
+        }
+        catch { /* best-effort */ }
+        return true;
+    }
+    catch {
+        return false;
+    }
+}
 /**
  * Check if the agent's CLI command is shadowed by a shell alias.
  *

package/dist/lib/state.d.ts

@@ -2,15 +2,17 @@
  * Filesystem layout and persistent state for agents-cli.
  *
  * Two roots:
- *  - ~/.agents-system/ — system repo (npm-shipped resources, versions, shims, backups, runs)
+ *  - ~/.agents-system/ — system repo (npm-shipped resources and canonical read-side defaults)
  *  - ~/.agents/        — user repo  (user-authored commands, skills, hooks, rules, mcp,
- *                                    permissions, subagents, profiles, secrets, agents.yaml)
+ *                                    permissions, subagents, profiles, secrets, agents.yaml,
+ *                                    packages, routines, runs, versions, shims, backups, plugins,
+ *                                    drive, trash)
  *
  * Resolution precedence for resources: project > user > system.
  * Every module that needs a path or reads/writes agents.yaml goes through here.
  */
 import type { Meta } from './types.js';
-/** Root of the system data directory (~/.agents-system/). Legacy alias — prefer getSystemAgentsDir(). */
+/** Root of the system data directory (~/.agents-system/). */
 export declare function getAgentsDir(): string;
 /** Root of the system data directory (~/.agents-system/). */
 export declare function getSystemAgentsDir(): string;
@@ -38,20 +40,7 @@ export declare function getHooksDir(): string;
 export declare function getSkillsDir(): string;
 /** Path to the canonical rules directory — system repo. */
 export declare function getRulesDir(): string;
-/** Back-compat export; resolves to system rules dir. */
-export declare function getMemoryDir(): string;
-/**
- * Read-side resolution for the canonical rules dir.
- *
- * Returns SYSTEM_RULES_DIR normally. Falls back to the legacy
- * SYSTEM_LEGACY_MEMORY_DIR (~/.agents-system/memory/) only when the upstream
- * still uses the old layout and the user hasn't pulled the rename yet —
- * detected by absence of rules/AGENTS.md and presence of memory/AGENTS.md.
- *
- * Prints a single warning per process the first time the fallback fires.
- * Per the read-only system-repo invariant, this never moves files; the rename
- * is applied when the user pulls upstream.
- */
+/** Read-side resolution for the canonical rules dir — system repo. */
 export declare function getResolvedRulesDir(): string;
 /** Path to MCP server YAML configs — system repo. */
 export declare function getMcpDir(): string;
@@ -59,8 +48,6 @@ export declare function getMcpDir(): string;
 export declare function getPermissionsDir(): string;
 /** Path to subagent definition directories — system repo. */
 export declare function getSubagentsDir(): string;
-/** Path to encrypted secret bundles — system repo. */
-export declare function getSecretsDir(): string;
 /** Path to ~/.agents-system/promptcuts.yaml. */
 export declare function getPromptcutsPath(): string;
 /** Path to the legacy MCP config JSON. */
@@ -74,7 +61,6 @@ export declare function getSystemRulesDir(): string;
 export declare function getSystemMcpDir(): string;
 export declare function getSystemPermissionsDir(): string;
 export declare function getSystemSubagentsDir(): string;
-export declare function getSystemSecretsDir(): string;
 export declare function getSystemPromptcutsPath(): string;
 export declare function getUserCommandsDir(): string;
 export declare function getUserHooksDir(): string;
@@ -85,22 +71,26 @@ export declare function getUserPermissionsDir(): string;
 export declare function getUserSubagentsDir(): string;
 export declare function getUserSecretsDir(): string;
 export declare function getUserPromptcutsPath(): string;
-/** Path to cloned packages (~/.agents-system/packages/). */
+/** Path to cloned packages (~/.agents/packages/). */
 export declare function getPackagesDir(): string;
-/** Path to routine YAML definitions (~/.agents-system/routines/). */
+/** Path to routine YAML definitions (~/.agents/routines/). */
 export declare function getRoutinesDir(): string;
-/** Path to routine execution logs (~/.agents-system/runs/). */
+/** Path to routine execution logs (~/.agents/runs/). */
 export declare function getRunsDir(): string;
-/** Path to installed agent CLI binaries (~/.agents-system/versions/). */
+/** Path to installed agent CLI binaries (~/.agents/versions/). */
 export declare function getVersionsDir(): string;
-/** Path to version-switching shim scripts (~/.agents-system/shims/). */
+/** Path to version-switching shim scripts (~/.agents/shims/). */
 export declare function getShimsDir(): string;
-/** Path to config backups (~/.agents-system/backups/). */
+/** Path to config backups (~/.agents/backups/). */
 export declare function getBackupsDir(): string;
-/** Path to plugin bundles (~/.agents-system/plugins/). */
+/** Path to plugin bundles (~/.agents/plugins/). */
 export declare function getPluginsDir(): string;
-/** Path to synced remote session data (~/.agents-system/drive/). */
+/** Path to synced remote session data (~/.agents/drive/). */
 export declare function getDriveDir(): string;
+/** Path to soft-deleted resources (~/.agents/trash/). */
+export declare function getTrashDir(): string;
+/** Path to soft-deleted version dirs (~/.agents/trash/versions/). */
+export declare function getTrashVersionsDir(): string;
 /**
  * Path to a single user-level extra DotAgent repo clone (~/.agents-<alias>/).
  *
@@ -136,3 +126,7 @@ import type { AgentId, ResourceType, VersionResources } from './types.js';
 export declare function recordVersionResources(agent: AgentId, version: string, resourceType: ResourceType, resources: string[]): void;
 export declare function getVersionResources(agent: AgentId, version: string): VersionResources | null;
 export declare function clearVersionResources(agent: AgentId, version: string): void;
+/** Active rules preset for an agent@version. Defaults to "default" when unset. */
+export declare function getActiveRulesPreset(agent: AgentId, version: string): string;
+/** Persist the active rules preset for an agent@version. */
+export declare function setActiveRulesPreset(agent: AgentId, version: string, preset: string): void;