Rewrite all import statements, patch() targets, sys.modules keys,
importlib.import_module() strings, and subprocess -m references to use
hermes_agent.* paths.
Strip sys.path.insert hacks from production code (rely on editable install).
Update COMPONENT_PREFIXES for logger filtering.
Fix 3 hardcoded getLogger() calls to use __name__.
Update transport and tool registry discovery paths.
Update plugin module path strings.
Add legacy process-name patterns for gateway PID detection.
Add main() to skills_sync for console_script entry point.
Fix _get_bundled_dir() path traversal after move.
Part of #14182, #14183
ShellFileOperations captured the terminal env's cwd at __init__ time and
used that stale value for every subsequent _exec() call. When the user
ran `cd` via the terminal tool, `env.cwd` updated but `ops.cwd` did not.
Relative paths passed to patch_replace / read_file / write_file / search
then targeted the ORIGINAL directory instead of the current one.
Observed symptom in agent sessions:
terminal: cd .worktrees/my-branch
patch hermes_cli/main.py <old> <new>
→ returns {"success": true} with a plausible unified diff
→ but `git diff` in the worktree shows nothing
→ the patch landed in the main repo's checkout of main.py instead
The diff looked legitimate because patch_replace computes it from the
IN-MEMORY content vs new_content, not by re-reading the file. The
write itself DID succeed — it just wrote to the wrong directory's copy
of the same-named file.
Fix: _exec() now resolves cwd from live sources in this order:
1. Explicit `cwd` arg (if provided by the caller)
2. Live `self.env.cwd` (tracks `cd` commands run via terminal)
3. Init-time `self.cwd` (fallback when env has no cwd attribute)
Includes a 5-test regression suite covering:
- cd followed by relative read follows live cwd
- the exact reported bug: patch_replace with relative path after cd
- explicit cwd= arg still wins over env.cwd
- env without cwd attribute falls back to init-time cwd
- patch_replace success reflects real file state (safety rail)
Co-authored-by: teknium1 <teknium@nousresearch.com>
