Summary

Salvages the substantive fix from #20864 by @liuhao1024 onto current main and closes #20856.

The bug: /branch (aka /fork) creates a new numbered branch session, but it vanishes from /resume and /sessions. Both surfaces funnel through list_sessions_rich(include_children=False), which hides any session with a parent_session_id unless it's identified as a branch via a heuristic — parent.end_reason == 'branched' AND child.started_at >= parent.ended_at.

That heuristic fails in two distinct ways:

1. CLI/gateway branches — work right after branching, but reopen_session() clears end_reason and a later end_session(parent, 'tui_shutdown') overwrites 'branched'. After the parent is resumed once and re-closed (routine), the heuristic stops matching and the branch is hidden permanently.
2. TUI branches (tui_gateway session.branch, the macOS desktop app's path) — the TUI never ends the parent as 'branched'; it creates the child while the parent is still live. So the heuristic never matched and TUI branches were hidden from the moment they were created. This is almost certainly the primary user-visible symptom.

The fix: persist a stable _branched_from marker in the branch session's model_config at creation time across all three branch paths (cli.py, gateway/run.py, and tui_gateway/server.py), and OR a json_extract(model_config, '$._branched_from') IS NOT NULL check into the list_sessions_rich filter. The marker is immutable across the parent's lifecycle, so the branch stays visible regardless of how (or whether) the parent is ended. The legacy end_reason='branched' heuristic is kept (OR'd) so branch sessions created before this change remain visible — no backward-compat regression. Subagent/compression children (no marker, parent not 'branched') stay correctly hidden.

Closes #20856.

Why a reimplementation rather than a cherry-pick

#20864 was a bundle of three unrelated fixes, 4826 commits behind main, and conflicting. Triaged each:

• WhatsApp npm timeout — already on main identically (1a4e8f704). Dropped.
• patch tool required list — marks mode-specific params as unconditionally required, contradicting its own "mode-specific" description; would break strict schema validators. Dropped.
• /branch visibility — the valuable one, salvaged here. The original PR only patched the CLI + gateway paths; this PR additionally covers the TUI path, which the original missed and which is the desktop app's primary surface.

The original couldn't cherry-pick (the /branch handlers and the list_sessions_rich filter all moved on main), so @liuhao1024's _branched_from approach was reimplemented on current main. Commit is attributed to them; the TUI extension and regression tests are the maintainer follow-up.

Verification

Reproduced the bug on current main across all paths, then confirmed the fix end-to-end (isolated HERMES_HOME, real SessionDB, and a handler-level E2E driving the actual session.branch RPC):

• tests/test_hermes_state.py::...::test_branch_session_visible_after_parent_reopen_and_reend — fails on main (assert 'branch' in ['parent']), passes here.
• tests/tui_gateway/test_protocol.py::test_session_branch_persists_branched_from_marker — fails on main (KeyError: 'model_config'), passes here. Drives the real session.branch handler and asserts the marker is persisted.
• tests/tui_gateway/ — 103 passed; tests/test_hermes_state.py + tests/cli/test_branch_command.py — 272 passed.
• ruff check clean on all changed files.

Credit

Approach and original fix by @liuhao1024 (#20864). Reimplemented on current main with authorship preserved; TUI branch-path coverage + regression tests added by the maintainer.