fix: sourcing login shell for linux breaking for installs. Apt install held by other process bug.

Author: test2

package.json

@@ -1,6 +1,6 @@
 {
   "name": "@codifycli/plugin-core",
-  "version": "1.2.6",
+  "version": "1.2.7",
   "description": "TypeScript library for building Codify plugins to manage system resources (applications, CLI tools, settings) through infrastructure-as-code",
   "main": "dist/index.js",
   "typings": "dist/index.d.ts",

src/pty/background-pty.ts

@@ -21,10 +21,12 @@ EventEmitter.defaultMaxListeners = 1000;
  */
 export class BackgroundPty implements IPty {
   private historyIgnore = Utils.getShell() === Shell.ZSH ? { HISTORY_IGNORE: '*' } : { HISTIGNORE: '*' };
-  // Login + interactive (-l -i) so the user's rc files are sourced. GUI launches
-  // (e.g. the Codify desktop app) do not inherit env like TART_HOME / PATH additions
-  // from the parent process; these live in ~/.zshrc / ~/.zprofile.
-  private basePty = pty.spawn(this.getDefaultShell(), ['-l', '-i'], {
+  // Add -l (login shell) only for GUI launches (e.g. the Codify desktop app),
+  // detected via the absence of process.env.SHELL, so rc files sourced via
+  // ~/.zshrc/~/.zprofile are picked up. On terminal/CI launches, avoid -l:
+  // it sources ~/.profile/~/.bash_profile instead of ~/.bashrc on Linux,
+  // hiding PATH exports written by FileUtils.addToShellRc().
+  private basePty = pty.spawn(this.getDefaultShell(), Utils.needsLoginShell() ? ['-l', '-i'] : ['-i'], {
     env: { ...process.env, ...this.historyIgnore },
     cols: 10_000, // Set to a really large value to prevent wrapping
     name: nanoid(6),

src/pty/seqeuntial-pty.ts

@@ -92,11 +92,13 @@ export class SequentialPty implements IPty {
       // the pty waiting for interactive input. Can't be disabled via env var; must unset the options explicitly.
       const disableAutocorrect = Utils.getShell() === Shell.ZSH ? 'unsetopt CORRECT CORRECT_ALL 2>/dev/null; ' : '';
       const wrappedCmd = `${disableAutocorrect}${cmd}`;
-      // Use a login + interactive shell (-l -i) so the user's rc files are sourced.
-      // This matters for GUI launches (e.g. the Codify desktop app) where env vars
-      // like TART_HOME and PATH additions live in ~/.zshrc/~/.zprofile and are not
-      // inherited from the parent process.
-      const args = options?.interactive ? ['-l', '-i', '-c', wrappedCmd] : ['-c', wrappedCmd]
+      // Add -l (login shell) only for GUI launches (e.g. the Codify desktop app),
+      // detected via the absence of process.env.SHELL, so rc files sourced via
+      // ~/.zshrc/~/.zprofile are picked up. On terminal/CI launches, avoid -l:
+      // it sources ~/.profile/~/.bash_profile instead of ~/.bashrc on Linux,
+      // hiding PATH exports written by FileUtils.addToShellRc().
+      const loginFlag = Utils.needsLoginShell() ? ['-l'] : [];
+      const args = options?.interactive ? [...loginFlag, '-i', '-c', wrappedCmd] : ['-c', wrappedCmd]
 
       // Run the command in a pty for interactivity
       const mPty = pty.spawn(this.getDefaultShell(), args, {

src/utils/index.ts

@@ -4,7 +4,7 @@ import * as fs from 'node:fs/promises';
 import os from 'node:os';
 import path from 'node:path';
 
-import { getPty, SpawnStatus } from '../pty/index.js';
+import { getPty, SpawnResult, SpawnStatus } from '../pty/index.js';
 
 export function isDebug(): boolean {
   return process.env.DEBUG != null && process.env.DEBUG.includes('codify'); // TODO: replace with debug library
@@ -146,6 +146,22 @@ export const Utils = {
     return process.env.SHELL || os.userInfo().shell || '/bin/zsh';
   },
 
+  /**
+   * Whether interactive spawns should add `-l` (login shell) on top of `-i`.
+   * Only needed when `process.env.SHELL` is unset — the signal that Codify was
+   * launched outside a terminal (e.g. the desktop app via launchd on macOS),
+   * where GUI-launched processes don't inherit the user's rc-file env (e.g.
+   * TART_HOME, PATH additions).
+   *
+   * When `SHELL` *is* set (normal terminal/CI launches), a login shell must be
+   * avoided: on Linux, `-l` sources `~/.profile`/`~/.bash_profile` instead of
+   * `~/.bashrc` (often not sourcing `.bashrc` at all, since CI images
+   * typically ship no `~/.bash_profile`), so PATH exports written by
+   * `FileUtils.addToShellRc()` become invisible to later interactive spawns.
+   */
+  needsLoginShell(): boolean {
+    return !process.env.SHELL;
+  },
 
   getPrimaryShellRc(): string {
     return this.getShellRcFiles()[0];
@@ -274,10 +290,25 @@ Brew can be installed using Codify:
       if (isAptInstalled.status === SpawnStatus.SUCCESS) {
         await $.spawn('apt-get update', { requiresRoot: true });
         const flagStr = extraFlags.length > 0 ? `${extraFlags.join(' ')} ` : '';
-        const { status, data } = await $.spawnSafe(`apt-get -y -qq install -o Dpkg::Use-Pty=0 -o Dpkg::Progress-Fancy=0 ${flagStr}${packageName}`, {
-          requiresRoot: true,
-          env: { DEBIAN_FRONTEND: 'noninteractive', NEEDRESTART_MODE: 'a' }
-        });
+
+        let status: SpawnResult['status'] = SpawnStatus.ERROR;
+        let data = '';
+        const maxLockRetries = 5;
+        for (let attempt = 0; attempt <= maxLockRetries; attempt++) {
+          ({ status, data } = await $.spawnSafe(`apt-get -y -qq install -o Dpkg::Use-Pty=0 -o Dpkg::Progress-Fancy=0 ${flagStr}${packageName}`, {
+            requiresRoot: true,
+            env: { DEBIAN_FRONTEND: 'noninteractive', NEEDRESTART_MODE: 'a' }
+          }));
+
+          // dpkg/apt lock is held by another process (e.g. unattended-upgrades on a fresh VM).
+          // This isn't a broken-dependency condition, so back off and retry rather than falling
+          // through to `apt-get install -f`, which will just hit the same lock and fail too.
+          const isLockContention = status === SpawnStatus.ERROR
+            && (data.includes('Could not get lock') || data.includes('dpkg frontend lock'));
+          if (!isLockContention || attempt === maxLockRetries) break;
+
+          await new Promise((resolve) => setTimeout(resolve, 5000 * (attempt + 1)));
+        }
 
         if (status === SpawnStatus.ERROR && data.includes('E: dpkg was interrupted, you must manually run \'sudo dpkg --configure -a\' to correct the problem.')) {
           await $.spawn('dpkg --configure -a', { requiresRoot: true });
@@ -288,6 +319,12 @@ Brew can be installed using Codify:
           return;
         }
 
+        const isLockContention = status === SpawnStatus.ERROR
+          && (data.includes('Could not get lock') || data.includes('dpkg frontend lock'));
+        if (isLockContention) {
+          throw new Error(`Failed to install package ${packageName} via apt: dpkg/apt lock held by another process after ${maxLockRetries} retries: ${data}`);
+        }
+
         if (status === SpawnStatus.ERROR) {
           // Attempt to fix broken dependencies then retry
           const fixResult = await $.spawnSafe('apt-get install -f -y -o Dpkg::Use-Pty=0 -o Dpkg::Progress-Fancy=0', {