fix: apply isolation namespace to shell execute cwd (#2329) [FaaFyfxR9WAQrL7FcAgEHJvztd8cVMxvjHRS55rw1nwH]

[waterWang]

Description

When IsolationScope.SESSION or IsolationScope.USER is configured, the LocalFilesystemWithShell correctly creates a namespace-aware working directory (e.g., <workspace>/<sessionId>/). However, the resolveExecuteCwd() method short-circuits when shellCwd is set (the project root), returning shellCwd directly without applying the namespace prefix. This causes shell commands to run in the project root instead of the isolated session directory, leading to failures when the agent tries to execute scripts that were generated in the isolated workspace.

Root Cause

In LocalFilesystemWithShell.resolveExecuteCwd():

if (shellCwd != null) {
    return shellCwd;  // ← BUG: skips namespace resolution entirely
}

When shellCwd is set (to the project root), the method returns immediately without checking the NamespaceFactory, so the shell always runs in the project root regardless of the configured isolation scope.

Fix

Use shellCwd (or getCwd() as fallback) as the base path, then apply namespace resolution on top of it:

Path base = shellCwd != null ? shellCwd : getCwd();
// ... then apply namespace on top of base

This ensures that when isolation scope is configured, the shell's working directory becomes <projectRoot>/<sessionId>/ (or <workspace>/<sessionId>/) instead of <projectRoot>/.

Testing

• The existing LocalFilesystemUserIsolationExampleTest and SandboxFilesystemIsolationScopeExampleTest should pass with this fix
• Commands executed via execute_shell_command will now correctly resolve to the isolated namespace directory

Fixes #2329

[gemini-code-assist]

Caution

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[codecov]

Codecov Report

❌ Patch coverage is 25.00000% with 3 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
...ent/filesystem/local/LocalFilesystemWithShell.java	25.00%	2 Missing and 1 partial ⚠️

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[oss-maintainer]

Summary

Fix correctly applies namespace isolation on top of shellCwd instead of bypassing it when shellCwd is set.

Analysis

Previously, resolveExecuteCwd() returned shellCwd directly when it was non-null, skipping namespace resolution entirely. This meant that under IsolationScope.SESSION or IsolationScope.USER, shell commands executed with an explicit shellCwd would escape the isolation namespace — a correctness bug.

The fix extracts a base path (preferring shellCwd over getCwd()) and then applies namespace segments on top, ensuring isolation is always enforced.

Verdict

Clean, minimal fix. Logic is correct. Build passes.

Note: #2434 appears to be a duplicate of this PR for the same issue (#2329). Consider closing one.