From 7eda5a69cc83bae2b78eaac8e37057f9a3180f0f Mon Sep 17 00:00:00 2001
From: teknium1 <127238744+teknium1@users.noreply.github.com>
Date: Wed, 23 Sep 2026 17:07:15 -0700
Subject: [PATCH] fix(update): a killed custom-branch merge is restored too,
 from every console script

On a custom branch the updater runs `git merge --no-edit origin/<branch>` inside the marker window.
Its files are the merge of both sides, a blob that is neither pre nor target, so the restore took
them for user edits: it put the upstream-only files back to pre, kept the merged ones and spent the
marker, leaving a mixed tree (a real random-kill of that merge: 104 of 500 trials broken).

- _early_recovery: when pre and target diverge, `git merge-tree --write-tree pre target` gives the
  tree the merge was writing; its blobs (and prefixes of them, for a file cut short) count as git's
  like the target's. Conflicted paths, and on git < 2.38 every path both sides changed, count as
  git's whatever their content. Paths with a newline are hashed one by one (`--stdin-paths` is
  newline-delimited). The docstring lists the by-design limits.
- run_agent (`hermes-agent`) and acp_adapter.entry (`hermes-acp`) never import hermes_cli.main, so
  they now run the same restore right after hermes_bootstrap (run_agent only when hermes_cli.main is
  not loaded, since it is also a library module).
- Tests: the second test kills inside a clean custom-branch merge (merged file, upstream-only file,
  a cut-short file, a user edit); the first pins that each console script's entry module imports
  no other checkout module before the restore runs. Both red on the previous head.
- evals/update_pipeline/interrupted_pull_ab.sh gains scenario E: a kill inside the custom-branch
  merge, then the `hermes-agent` import.
---
 acp_adapter/entry.py                          |   7 ++
 evals/update_pipeline/interrupted_pull_ab.sh  |  42 ++++++-
 hermes_cli/_early_recovery.py                 | 106 ++++++++++++------
 run_agent.py                                  |  11 +-
 .../test_update_interrupted_pull.py           |  53 ++++++++-
 5 files changed, 177 insertions(+), 42 deletions(-)

diff --git a/acp_adapter/entry.py b/acp_adapter/entry.py
index 0851ad1676..fc3386f034 100644
--- a/acp_adapter/entry.py
+++ b/acp_adapter/entry.py
@@ -20,6 +20,13 @@ else:
     # Stop a ``utils/``/``proxy/``/``ui/`` package in the launch cwd from shadowing Hermes modules.
     hermes_bootstrap.harden_import_path()
 
+# `hermes-acp` runs without hermes_cli.main: repair a `hermes update` killed mid-pull here, before
+# importing anything else from the checkout (a no-op under `hermes acp`, which already did).
+from hermes_cli import _early_recovery
+
+if _early_recovery.restore_interrupted_pull():
+    _early_recovery.relaunch_after_restore()
+
 import argparse
 import asyncio
 import logging
diff --git a/evals/update_pipeline/interrupted_pull_ab.sh b/evals/update_pipeline/interrupted_pull_ab.sh
index 87c6b937af..c923763265 100755
--- a/evals/update_pipeline/interrupted_pull_ab.sh
+++ b/evals/update_pipeline/interrupted_pull_ab.sh
@@ -4,14 +4,15 @@
 #   evals/update_pipeline/interrupted_pull_ab.sh <repo> <installed-sha> <label> [python]
 #
 # Builds a disposable origin + install at <installed-sha>; origin/main gets one commit that changes
-# utils.py, makes hermes_cli/config.py import a new utils name, changes run_agent.py and adds a
-# package. Runs the REAL autostash + _pull_updates from the install's own tree and the REAL entry point
+# utils.py, makes hermes_cli/config.py and run_agent.py import a new utils name, and adds a package. Runs the REAL autostash + _pull_updates from the install's own tree and the REAL entry point
 # (`python -m hermes_cli.main config path`) under a disposable HOME/HERMES_HOME:
 #   A  updater SIGKILLed before git wrote anything; user edits upstream-changed files, fetches, runs hermes
 #   B  custom branch whose commit conflicts upstream: update exits 1; user merges by hand, runs hermes
 #   C  git wrote config.py + the new package, SIGKILL; user edits an upstream-changed file git never wrote
 #   D  C in a linked-worktree install (`.git` is a file)
-# Fixed: A/B untouched, C/D restored with the user edit kept and the re-update lands; one VERDICT line.
+#   E  custom branch whose commit merges cleanly: the kill lands inside the `git merge`, after it wrote
+#      the merged run_agent.py; the user edits a file git never wrote, then runs `hermes-agent`'s import
+# Fixed: A/B untouched, C/D/E restored with the user edit kept and the re-update lands; one VERDICT line.
 # [python] defaults to <repo>/venv/bin/python (needs the Hermes deps).
 set -u
 REPO=$1; REF=$2; LABEL=$3
@@ -48,7 +49,7 @@ setup() {  # $1 = install kind: clone | worktree
     printf '\n\ndef _torn_probe():\n    return 1\n' >> utils.py
     sed -i 's/^from utils import atomic_replace, fast_safe_load, file_signature$/from utils import atomic_replace, fast_safe_load, file_signature, _torn_probe  # noqa: F401/' hermes_cli/config.py
     grep -q _torn_probe hermes_cli/config.py || { echo "SETUP: config.py import line not found"; exit 1; }
-    echo "# upstream change" >> run_agent.py
+    echo "from utils import _torn_probe  # noqa: E402,F401" >> run_agent.py
     mkdir -p torn_newpkg && echo "from utils import _torn_probe" > torn_newpkg/__init__.py
     git add -A && git commit -qm "upstream B" )
   if [ "$1" = worktree ]; then
@@ -141,7 +142,36 @@ EOF
   echo "  after re-update: HEAD==origin/main? $([ "$(git rev-parse HEAD)" = "$(git rev-parse origin/main)" ] && echo yes || echo no) user edit kept=$(grep -c USER_EDIT run_agent.py)"
   [ "$(git rev-parse HEAD)" = "$(git rev-parse origin/main)" ] && [ "$(grep -c USER_EDIT run_agent.py)" = 1 ] && CD_OK=$((CD_OK + 1))
 done
+# ---- E: the custom-branch `git merge` wrote its merged run_agent.py, SIGKILL; `hermes-agent` launches ----
+echo; echo "--- E: kill inside the custom-branch merge, then the hermes-agent entry point (run_agent)"
+setup clone >/dev/null
+git checkout -q -b mywork && sed -i "1a LOCAL_WORK = 1" run_agent.py && git commit -qam "local work that merges cleanly"
+cat > "$U/fakebin/git" <<'EOF'
+#!/bin/bash
+# The merge writes run_agent.py as the merge of both sides (upstream's half imports a utils name git has
+# not written yet), holds index.lock, and is SIGKILLed.
+for a in "$@"; do
+  if [ "$a" = "--no-edit" ]; then
+    /usr/bin/git show "$(/usr/bin/git merge-tree --write-tree HEAD origin/main):run_agent.py" > run_agent.py
+    touch "$(/usr/bin/git rev-parse --git-dir)/index.lock"
+    sleep 30
+  fi
+done
+exec /usr/bin/git "$@"
+EOF
+chmod +x "$U/fakebin/git"
+PID=$(pull_bg); for i in $(seq 60); do grep -q _torn_probe run_agent.py && break; sleep 0.5; done; sleep 1
+kill -KILL -- -$PID; wait $PID 2>/dev/null
+echo "  torn: HEAD=$(git rev-parse --short HEAD) [$(git status --porcelain | tr '\n' ' ')] marker=[$(marker | cut -c1-60)...]"
+sed -i '2a MY_UNCOMMITTED_WORK = 42' utils.py  # upstream changes this file too; git never wrote it
+PYTHONPATH=$U/install timeout 120 "$PY" -c "import run_agent; print('run_agent imported')" 2>&1 | grep -v '^$' | tail -4 | sed 's/^/    hermes-agent> /'
+echo "  RESULT E: [$(git status --porcelain | tr '\n' ' ')] user edit kept=$(grep -c MY_UNCOMMITTED_WORK utils.py) marker=[$(marker)]"
+PATH=/usr/bin:$PATH $PY $U/pull.py $U/install 2>&1 | grep PULL | sed 's/^/    re-update> /'
+E_MERGED=$(git merge-base --is-ancestor origin/main HEAD && grep -q LOCAL_WORK run_agent.py && echo yes || echo no)
+echo "  after re-update: origin/main merged with the local commit? $E_MERGED user edit kept=$(grep -c MY_UNCOMMITTED_WORK utils.py)"
+E_OK=$([ "$E_MERGED" = yes ] && [ "$(grep -c MY_UNCOMMITTED_WORK utils.py)" = 1 ] && echo 1 || echo 0)
+
 echo
-if [ "$A_OK$B_OK$CD_OK" = 112 ]; then echo "VERDICT: FIXED ($LABEL) — user work untouched in A/B, torn tree restored with user edits kept in C/D"
-else echo "VERDICT: FIRES ($LABEL) — A_ok=$A_OK B_ok=$B_OK CD_ok=$CD_OK/2"; fi
+if [ "$A_OK$B_OK$CD_OK$E_OK" = 1121 ]; then echo "VERDICT: FIXED ($LABEL) — user work untouched in A/B, torn tree restored with user edits kept in C/D/E"
+else echo "VERDICT: FIRES ($LABEL) — A_ok=$A_OK B_ok=$B_OK CD_ok=$CD_OK/2 E_ok=$E_OK"; fi
 rm -rf "$U"
diff --git a/hermes_cli/_early_recovery.py b/hermes_cli/_early_recovery.py
index 32d522868a..d02cb72db4 100644
--- a/hermes_cli/_early_recovery.py
+++ b/hermes_cli/_early_recovery.py
@@ -237,47 +237,81 @@ def interrupted_pull_marker(root: Path) -> Path:
     return _git_dir(root) / INTERRUPTED_PULL_MARKER
 
 
+def _trees_git_could_write(git, pre: str, target: str) -> tuple[list[str], set[str]]:
+    """The trees the killed git was moving the checkout to, and the paths whose new content is unknowable.
+
+    A fast-forward or ``reset --hard`` writes ``target``. On a custom branch the updater runs
+    ``git merge``, whose files are the merge of both sides: ``merge-tree`` computes the same tree. A
+    conflicted path (its markers carry other labels) and, on git < 2.38 (no ``--write-tree``), every
+    path both sides changed count as git's whatever their content.
+    """
+    base = git("merge-base", pre, target).stdout.strip()
+    if not base or base == pre:  # fast-forward, or unrelated histories (only a reset can land those)
+        return [target], set()
+    merged = git("merge-tree", "--write-tree", "-z", "--name-only", "--no-messages", pre, target)
+    if merged.returncode in (0, 1):  # 1: conflicts
+        tree, *conflicted = merged.stdout.split("\0")
+        return [target, tree], set(filter(None, conflicted))
+    changed = [set(filter(None, git("diff", "--name-only", "-z", "--no-renames", base, side).stdout.split("\0")))
+               for side in (pre, target)]
+    return [target], changed[0] & changed[1]
+
+
+def _hash_worktree(git, paths: list[str]) -> dict[str, str]:
+    """Blob ids of the checkout's files, through the repo's clean filters, like ``git add`` would store."""
+    listed = [p for p in paths if "\n" not in p]  # --stdin-paths is newline-delimited
+    blobs = {}
+    if listed:
+        hashed = git("hash-object", "--stdin-paths", stdin="\n".join(listed) + "\n")
+        if hashed.returncode != 0:
+            raise subprocess.SubprocessError(hashed.stderr.strip())
+        blobs.update(zip(listed, hashed.stdout.split()))
+    for path in set(paths) - set(listed):
+        blobs[path] = git("hash-object", "--", path).stdout.strip()
+    return blobs
+
+
 def _paths_git_wrote(git, root: Path, pre: str, target: str) -> tuple[list[str], list[str]] | None:
     """Paths the killed git already touched on the way to ``target``: (restore from HEAD, delete as added).
 
     Git rewrites a file as unlink, create, write, so a kill leaves it missing, empty or cut short:
-    all of those count as git's, like the full ``target`` blob. Content that matches neither side and
-    is not the start of the target is the user's own edit (e.g. a re-applied stash) and is left
-    alone. ``None``: git no longer knows ``target``.
+    all of those count as git's, like the full new blob. Content that matches neither side and is not
+    the start of a new blob is the user's own edit (e.g. a re-applied stash) and is left alone.
+    ``None``: git no longer knows ``target``.
     """
-    diff = git("diff", "--raw", "-z", "--no-renames", "--no-abbrev", pre, target)
-    if diff.returncode != 0:
+    if git("rev-parse", "-q", "--verify", f"{target}^{{commit}}").returncode != 0:
         return None
-    parts = diff.stdout.split("\0")
-    entries = []  # (status, path, pre mode, pre blob, target blob)
-    for meta, path in zip(parts[::2], parts[1::2]):
-        old_mode, new_mode, old_blob, new_blob, status = meta.lstrip(":").split()
-        if status == "D" and old_mode in _REGULAR_FILE_MODES:
-            entries.append((status, path, old_mode, old_blob, None))
-        elif status != "D" and new_mode in _REGULAR_FILE_MODES:
-            entries.append((status, path, old_mode, old_blob, new_blob))
-    present = [path for _s, path, _m, _o, blob in entries if blob and (root / path).is_file()]
-    hashed = git("hash-object", "--stdin-paths", stdin="\n".join(present) + "\n") if present else None
-    if hashed is not None and hashed.returncode != 0:
-        raise subprocess.SubprocessError(hashed.stderr.strip())
-    worktree_blob = dict(zip(present, hashed.stdout.split() if hashed else ()))
+    trees, unknown = _trees_git_could_write(git, pre, target)
+    entries = {}  # path -> (pre mode, pre blob or None when git adds it, [(new mode, new blob or None)])
+    for tree in trees:
+        diff = git("diff", "--raw", "-z", "--no-renames", "--no-abbrev", pre, tree)
+        if diff.returncode != 0:
+            raise subprocess.SubprocessError(diff.stderr.strip())
+        parts = diff.stdout.split("\0")
+        for meta, path in zip(parts[::2], parts[1::2]):
+            old_mode, new_mode, old_blob, new_blob, status = meta.lstrip(":").split()
+            if (old_mode if status == "D" else new_mode) not in _REGULAR_FILE_MODES:
+                continue
+            entry = entries.setdefault(path, (old_mode, None if status == "A" else old_blob, []))
+            entry[2].append((new_mode, None if status == "D" else new_blob))
+    worktree_blob = _hash_worktree(git, [path for path in entries if (root / path).is_file()])
     restore, added = [], []
-    for status, path, old_mode, old_blob, blob in entries:
-        file = root / path
-        if blob is None:
-            written = not file.exists()
-        elif path not in worktree_blob:
-            written = status != "A"  # unlinked, not yet recreated
-        elif worktree_blob[path] not in (old_blob, blob):  # git's own file, cut short, starts the target
-            smudged = subprocess.run(["git", "-C", str(root), "cat-file", "--filters", f"--path={path}", blob],
-                                     capture_output=True, check=True, timeout=120, stdin=subprocess.DEVNULL)
-            written = smudged.stdout.startswith(file.read_bytes())
-        elif old_blob == blob:  # mode-only: only the exec bit tells whether git got here
-            written = sys.platform != "win32" and bool(file.stat().st_mode & 0o100) != (old_mode == "100755")
-        else:
-            written = worktree_blob[path] == blob
+    for path, (old_mode, old_blob, new) in entries.items():
+        file, blobs = root / path, {blob for _mode, blob in new if blob}
+        if path not in worktree_blob:
+            written = old_blob is not None  # unlinked (or deleted), not yet recreated
+        elif worktree_blob[path] == old_blob:  # only a mode change tells whether git got here
+            written = (sys.platform != "win32" and any(b == old_blob and m != old_mode for m, b in new)
+                       and bool(file.stat().st_mode & 0o100) != (old_mode == "100755"))
+        elif worktree_blob[path] in blobs or path in unknown:
+            written = True
+        else:  # git's own file cut short starts one of the new blobs
+            content = file.read_bytes()
+            written = any(subprocess.run(["git", "-C", str(root), "cat-file", "--filters", f"--path={path}", blob],
+                                         capture_output=True, check=True, timeout=120,
+                                         stdin=subprocess.DEVNULL).stdout.startswith(content) for blob in blobs)
         if written:
-            (added if status == "A" else restore).append(path)
+            (added if old_blob is None else restore).append(path)
     return restore, added
 
 
@@ -292,6 +326,12 @@ def restore_interrupted_pull(project_root: Path | None = None) -> bool:
     (the target's content, or torn on the way there) returns to HEAD (the commit the venv was built
     for), so the install is whole again and ``hermes update`` redoes the update from the start. Local
     edits are never touched; the updater's autostash (if any) stays in ``git stash list``.
+
+    Limits, by design: a torn ``hermes_cli/__init__.py`` or ``hermes_bootstrap.py`` fails before this
+    runs (``git -C <root> reset --hard <pre>`` from the marker repairs it). A file git also changes
+    that the user deleted, emptied or cut to a prefix of git's version looks exactly like git's own
+    half-written file and is restored too, as is a user edit to a conflicted path or, on git < 2.38, to a
+    path both sides of a custom-branch merge changed.
     """
     try:
         root = _project_root() if project_root is None else project_root
diff --git a/run_agent.py b/run_agent.py
index 032a5e7669..bb01bfa06f 100644
--- a/run_agent.py
+++ b/run_agent.py
@@ -12,12 +12,21 @@ try:
 except ModuleNotFoundError:
     pass  # partial `hermes update` — only skips the Windows UTF-8 stdio setup
 
+import sys
+
+# `hermes-agent` runs this module without hermes_cli.main, which repairs a `hermes update` killed
+# while git wrote the new tree; do it here, before importing anything else from the checkout.
+if "hermes_cli.main" not in sys.modules:
+    from hermes_cli import _early_recovery
+
+    if _early_recovery.restore_interrupted_pull():
+        _early_recovery.relaunch_after_restore()
+
 import json
 import logging
 logger = logging.getLogger(__name__)
 import os
 import re
-import sys
 import time
 import threading
 import uuid
diff --git a/tests/hermes_cli/test_update_interrupted_pull.py b/tests/hermes_cli/test_update_interrupted_pull.py
index 394d836263..5aac616b2e 100644
--- a/tests/hermes_cli/test_update_interrupted_pull.py
+++ b/tests/hermes_cli/test_update_interrupted_pull.py
@@ -24,6 +24,29 @@ def _git(root: Path, *args: str) -> str:
                           text=True, encoding="utf-8").stdout.strip()
 
 
+_MULTI = "top = 1\nx = 0\ny = 0\nz = 0\nend = 1\n"
+
+
+# Runs an entry module with the repair replaced by a probe that lists the checkout modules imported so
+# far (the entry module, its packages and what hermes_bootstrap needs excluded), then stops.
+_ENTRY_SPY = """
+import importlib, json, os, sys
+import hermes_bootstrap
+from hermes_cli import _early_recovery as er
+
+before, venv, entry = set(sys.modules), os.path.realpath(sys.prefix), sys.argv[1]
+
+def probe():
+    loaded = (n for n in set(sys.modules) - before if not f"{entry}.".startswith(n + "."))
+    files = {n: os.path.realpath(str(getattr(sys.modules[n], "__file__", None))) for n in loaded}
+    print(json.dumps(sorted(n for n, f in files.items() if f.startswith(os.getcwd()) and not f.startswith(venv))))
+    raise SystemExit(0)
+
+er.restore_interrupted_pull = probe
+importlib.import_module(entry)
+"""
+
+
 @pytest.fixture
 def checkout(tmp_path, monkeypatch):
     """An install at commit A whose fetched ``origin/main`` is B (modifies, deletes, adds, flips a mode)."""
@@ -33,12 +56,12 @@ def checkout(tmp_path, monkeypatch):
     _git(origin, "config", "user.email", "t@example.invalid")
     _git(origin, "config", "user.name", "t")
     files = {"utils.py": "OLD = 1\n", "other.py": "a = 1\n", "gone.py": "x = 1\n", "cut.py": "c = 1\n",
-             "blank.py": "b = 1\n", "half.py": "h = 1\n", "tool.sh": "echo\n"}
+             "blank.py": "b = 1\n", "half.py": "h = 1\n", "tool.sh": "echo\n", "multi.py": _MULTI}
     for name, body in files.items():
         (origin / name).write_text(body, encoding="utf-8", newline="")
     _git(origin, "add", "-A")
     _git(origin, "commit", "-qm", "A")
-    for name, body in {"utils.py": "NEW = 1\n", "other.py": "a = 2\n", "cut.py": "c = 2\n",
+    for name, body in {"utils.py": "NEW = 1\n", "other.py": "a = 2\n", "cut.py": "c = 2\n", "multi.py": "top = 2\n" + _MULTI[8:],
                        "blank.py": "b = 2\n", "half.py": "h = 2  # long enough to span pages\n"}.items():
         (origin / name).write_text(body, encoding="utf-8", newline="")
     (origin / "gone.py").unlink()
@@ -111,6 +134,14 @@ def test_killed_pull_is_restored_on_next_launch_and_update_reruns(checkout, monk
     _pull(root)  # `hermes update` again: a normal fast-forward
     assert _git(root, "rev-parse", "HEAD") == b and not marker.exists()
 
+    # Every console script (`hermes`, `hermes-agent`, `hermes-acp`) repairs before its entry module imports
+    # any other checkout module past hermes_bootstrap: any of them may be a half-written file.
+    repo = os.path.realpath(Path(er.__file__).parent.parent)
+    for entry in ("hermes_cli.main", "run_agent", "acp_adapter.entry"):
+        run = subprocess.run([sys.executable, "-c", _ENTRY_SPY, entry], cwd=repo, capture_output=True, text=True,
+                             encoding="utf-8", env={**os.environ, "PYTHONPATH": repo}, timeout=120)
+        assert run.stdout.strip().splitlines()[-1:] == ["[]"], (entry, run.stdout[-500:], run.stderr[-2000:])
+
 
 def test_restore_never_touches_user_work_when_git_wrote_nothing(checkout):
     """sys.exit on a merge conflict is not a kill, and a marker git never acted on restores nothing."""
@@ -145,3 +176,21 @@ def test_restore_never_touches_user_work_when_git_wrote_nothing(checkout):
     # A target git no longer knows (gc, re-clone) can never be compared against: drop the marker.
     marker.write_text(stale.replace(b, "0" * 40), encoding="utf-8", newline="")
     assert er.restore_interrupted_pull(root) is False and not marker.exists()
+
+    # Killed inside the custom-branch `git merge`: its files are the merge of both sides, not origin's
+    # blob, and still git's (torn ones too), while the user's own edit survives.
+    _git(root, "reset", "-q", "--hard", a)
+    (root / "multi.py").write_text(_MULTI.replace("end = 1", "end = 'mine'"), encoding="utf-8", newline="")
+    _git(root, "commit", "-qam", "local work that merges cleanly")
+    pre = _git(root, "rev-parse", "HEAD")
+    merged = _git(root, "merge-tree", "--write-tree", pre, b)
+    merged_multi = _git(root, "show", f"{merged}:multi.py") + "\n"
+    assert merged_multi == "top = 2\nx = 0\ny = 0\nz = 0\nend = 'mine'\n"  # neither side's blob
+    (root / "multi.py").write_text(merged_multi, encoding="utf-8", newline="")
+    (root / "utils.py").write_text("NEW = 1\n", encoding="utf-8", newline="")
+    (root / "half.py").write_bytes(b"h = 2  # long")
+    (root / "other.py").write_text("a = 1  # my edit\n", encoding="utf-8", newline="")
+    marker.write_text(f"pid=0\npre={pre}\ntarget={b}\nstash=\n", encoding="utf-8", newline="")
+    assert er.restore_interrupted_pull(root) is True
+    assert _git(root, "rev-parse", "HEAD") == pre and not marker.exists()
+    assert _git(root, "status", "--porcelain", "--untracked-files=all") == "M other.py"