Fix extraction races, installer reliability, and failing CI

.github/workflows/ci.yml

@@ -9,8 +9,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Install shellcheck
-        run: sudo apt-get install -y shellcheck
+      - name: Install test tools
+        run: sudo apt-get install -y shellcheck tmux
       - run: make check
 
   macos-test:

CHANGELOG.md

@@ -1,5 +1,26 @@
 # Changelog
 
+## Unreleased
+
+### Fixed
+- Restore Linux CI by explicitly quoting empty `CDPATH` assignments.
+- Preserve the order of multiple text blocks within an assistant message and
+  skip malformed message fields without losing the rest of the answer.
+- Retry missing or disappearing transcripts during settling, retaining text
+  already read and falling back to the Stop payload at the deadline.
+- Give overlapping hook writes separate atomic temporary files; store answers
+  with owner-only permissions.
+- Quote hook and tmux commands for repository paths containing shell syntax,
+  including when upgrading existing installations.
+- Keep repeated installs idempotent when `set-clipboard` is off; preserve
+  settings permissions and unrelated hooks on install and uninstall.
+- Remove tmux bindings even if tmux has been removed, avoid creating config
+  during uninstall, and replace the `kill-server` advice with `unbind-key y`.
+
+### Added
+- Regression tests for extraction races and installer behavior in disposable
+  homes, including a real tmux configuration/parser check on Linux CI.
+
 ## 0.2.0 — 2026-09-14
 
 ### Changed

Makefile

@@ -17,10 +17,10 @@ lint:
 		echo "lint: shellcheck not installed, skipping shell lint"; \
 	fi
 	@if python3 -m pyflakes --version >/dev/null 2>&1; then \
-		python3 -m pyflakes hooks/extract.py tests/test_extract.py; \
+		python3 -m pyflakes hooks/extract.py tests/*.py; \
 	else \
 		echo "lint: pyflakes not installed, falling back to py_compile"; \
-		python3 -m py_compile hooks/extract.py; \
+		python3 -m py_compile hooks/extract.py tests/*.py; \
 	fi
 
 check: lint test

README.md

@@ -168,7 +168,10 @@ make lint     # shellcheck, when installed
 The tests build synthetic transcripts and drive the hook the way Claude Code
 does (payload on stdin, `TMUX_PANE` in the environment), including the case
 where the transcript is still behind when the hook fires. CI runs them on
-Linux and macOS. Changes are listed in [CHANGELOG.md](CHANGELOG.md).
+Linux and macOS. Installer tests use disposable homes and preserve the real
+user's configuration. When tmux is installed, they also verify the generated
+binding with an isolated tmux server; Linux CI includes this check.
+Changes are listed in [CHANGELOG.md](CHANGELOG.md).
 
 ## License
 

docs/DESIGN.md

@@ -67,8 +67,9 @@ One JSON object per line. Measured shape:
 
 Four things this dictates:
 
-1. **One content block per assistant line.** An answer is spread across many
-   lines, so all of them must be collected and re-joined in order.
+1. **One assistant message per line.** An answer can span many lines and a
+   message can hold several text blocks. Collect messages in chronological
+   order while preserving the order of the blocks within each message.
 2. **Tool results are `user` entries.** Naively stopping at the first `user`
    entry truncates every answer that used a tool. The boundary test is "a
    `user` entry containing at least one non-`tool_result` block".

hooks/extract.py

@@ -12,6 +12,7 @@
 import json
 import os
 import sys
+import tempfile
 import time
 
 VERSION = "0.2.0"
@@ -55,7 +56,8 @@ def iter_lines_reverse(path, chunk_size=CHUNK):
 
 
 def blocks_of(entry):
-    content = (entry.get("message") or {}).get("content")
+    message = entry.get("message")
+    content = message.get("content") if isinstance(message, dict) else None
     if isinstance(content, list):
         return [b for b in content if isinstance(b, dict)]
     if isinstance(content, str):
@@ -92,12 +94,17 @@ def extract_answer(lines):
 
         kind = entry.get("type")
         if kind == "assistant":
+            message_parts = []
             for block in blocks_of(entry):
                 # thinking and tool_use are not the answer.
-                if block.get("type") == "text":
-                    text = (block.get("text") or "").strip()
+                if block.get("type") == "text" and isinstance(block.get("text"), str):
+                    text = block["text"].strip()
                     if text:
-                        parts.append(text)
+                        message_parts.append(text)
+            # Only entries run backwards; blocks within an entry are already
+            # chronological and must stay together when parts is reversed.
+            if message_parts:
+                parts.append("\n\n".join(message_parts))
         elif kind == "user":
             if is_human_turn(entry):
                 break
@@ -147,9 +154,8 @@ def caught_up(answer, last_message):
     The hook payload carries that block as `last_assistant_message`; when the
     extracted answer ends with it, nothing more is coming.
     """
-    if not last_message:
-        return False
-    return squash(answer).endswith(squash(last_message))
+    final_text = squash(last_message or "")
+    return bool(final_text) and squash(answer).endswith(final_text)
 
 
 def settle(path, last_message, max_wait=None):
@@ -165,6 +171,7 @@ def settle(path, last_message, max_wait=None):
     """
     if max_wait is None:
         max_wait = SETTLE_MAX
+    last_message = (last_message or "").strip()
     deadline = time.monotonic() + max_wait
     answer = ""
     size = None
@@ -175,9 +182,17 @@ def settle(path, last_message, max_wait=None):
         except OSError:
             current = -1
         if current != size:
-            size = current
             quiet = 0
-            answer = extract_answer(iter_lines_reverse(path))
+            try:
+                candidate = extract_answer(iter_lines_reverse(path)) if current >= 0 else answer
+            except OSError:
+                # The file may disappear between stat and open. Retry even
+                # if it comes back with the same size, retaining any text
+                # already read so complete() can still add the final block.
+                size = None
+            else:
+                size = current
+                answer = candidate
             if caught_up(answer, last_message):
                 return answer
         else:
@@ -219,12 +234,19 @@ def log_error(exc):
 
 
 def write_answer(text, dest):
-    os.makedirs(os.path.dirname(dest), exist_ok=True)
-    tmp = dest + ".tmp"
-    with open(tmp, "w", encoding="utf-8") as fh:
-        fh.write(text)
-    # Atomic: a keypress landing mid-write must not read a half-written file.
-    os.replace(tmp, dest)
+    directory = os.path.dirname(dest)
+    os.makedirs(directory, mode=0o700, exist_ok=True)
+    # Overlapping hooks need separate temporary files. mkstemp also keeps
+    # answers private (0600) regardless of the user's umask.
+    fd, tmp = tempfile.mkstemp(prefix=os.path.basename(dest) + ".", suffix=".tmp", dir=directory)
+    try:
+        with os.fdopen(fd, "w", encoding="utf-8") as fh:
+            fh.write(text)
+        # A keypress landing mid-write must not read a half-written file.
+        os.replace(tmp, dest)
+    finally:
+        if os.path.exists(tmp):
+            os.remove(tmp)
 
 
 def prune(keep_days=KEEP_DAYS, now=None):
@@ -278,7 +300,7 @@ def main():
         transcript = payload.get("transcript_path")
         last_message = payload.get("last_assistant_message")
 
-    if not transcript or not os.path.exists(transcript):
+    if not transcript:
         # The payload still carries the final block; better than nothing.
         answer = complete("", last_message)
     else:

install.sh

@@ -8,7 +8,7 @@
 
 set -eu
 
-REPO=$(CDPATH= cd -- "$(dirname -- "$0")" && pwd)
+REPO=$(CDPATH='' cd -- "$(dirname -- "$0")" && pwd)
 SETTINGS="$HOME/.claude/settings.json"
 TMUX_CONF="$HOME/.tmux.conf"
 MARK_BEGIN="# >>> cc-yank >>>"
@@ -24,30 +24,37 @@ command -v python3 >/dev/null 2>&1 || {
     echo "cc-yank: python3 is required (stdlib only, no packages)." >&2
     exit 1
 }
-chmod +x "$REPO/hooks/extract.py" "$REPO/bin/cc-yank"
+if [ "$uninstall" -eq 0 ]; then
+    chmod +x "$REPO/hooks/extract.py" "$REPO/bin/cc-yank"
+fi
 
 # ---------------------------------------------------- ~/.claude/settings.json
 # Merged with python3 rather than sed: this file holds the user's whole
 # configuration and a botched edit costs them more than this tool is worth.
 echo "settings.json"
-if [ ! -f "$SETTINGS" ]; then
-    mkdir -p "$(dirname "$SETTINGS")"
-    printf '{}\n' > "$SETTINGS"
-    say "created $SETTINGS"
-fi
-
 python3 - "$SETTINGS" "$REPO/hooks/extract.py" "$uninstall" <<'PY'
-import json, os, shutil, sys, time
+import json, os, shlex, shutil, sys, time
 
 path, hook, uninstall = sys.argv[1], sys.argv[2], sys.argv[3] == "1"
-command = '"%s"' % hook
+command = shlex.quote(hook)
+# Recognize commands written by older installers as well.
+commands = {command, hook, '"%s"' % hook}
+
+if not os.path.isfile(path):
+    if uninstall:
+        print("  no cc-yank hook registered")
+        sys.exit(0)
+    os.makedirs(os.path.dirname(path), exist_ok=True)
+    with open(path, "w") as fh:
+        fh.write("{}\n")
+    print("  created %s" % path)
 
 with open(path) as fh:
     settings = json.load(fh)
 
 stop = settings.setdefault("hooks", {}).setdefault("Stop", [])
 present = any(
-    h.get("command") in (command, hook)
+    h.get("command") in commands
     for entry in stop for h in entry.get("hooks", [])
 )
 
@@ -57,15 +64,23 @@ if uninstall:
         sys.exit(0)
     for entry in stop:
         entry["hooks"] = [
-            h for h in entry.get("hooks", []) if h.get("command") not in (command, hook)
+            h for h in entry.get("hooks", []) if h.get("command") not in commands
         ]
     settings["hooks"]["Stop"] = [e for e in stop if e.get("hooks")]
     if not settings["hooks"]["Stop"]:
         del settings["hooks"]["Stop"]
     action = "removed Stop hook"
 elif present:
-    print("  Stop hook already registered")
-    sys.exit(0)
+    changed = False
+    for entry in stop:
+        for h in entry.get("hooks", []):
+            if h.get("command") in commands and h["command"] != command:
+                h["command"] = command
+                changed = True
+    if not changed:
+        print("  Stop hook already registered")
+        sys.exit(0)
+    action = "updated Stop hook quoting"
 else:
     stop.append({"hooks": [{"type": "command", "command": command}]})
     action = "registered Stop hook"
@@ -82,16 +97,14 @@ tmp = path + ".tmp"
 with open(tmp, "w") as fh:
     json.dump(settings, fh, indent=2, ensure_ascii=False)
     fh.write("\n")
+shutil.copymode(path, tmp)
 os.replace(tmp, path)
 print("  %s (backup: %s)" % (action, os.path.basename(backup)))
 PY
 
 # ------------------------------------------------------------- ~/.tmux.conf
 echo "tmux"
-if ! command -v tmux >/dev/null 2>&1; then
-    say "tmux not installed — the keybinding is unavailable."
-    say "cc-yank still works as a CLI: $REPO/bin/cc-yank"
-elif [ "$uninstall" -eq 1 ]; then
+if [ "$uninstall" -eq 1 ]; then
     if [ -f "$TMUX_CONF" ] && grep -qF "$MARK_BEGIN" "$TMUX_CONF"; then
         tmp=$(mktemp)
         sed "/^$MARK_BEGIN\$/,/^$MARK_END\$/d" "$TMUX_CONF" > "$tmp"
@@ -100,34 +113,75 @@ elif [ "$uninstall" -eq 1 ]; then
     else
         say "no cc-yank binding found"
     fi
-elif [ -f "$TMUX_CONF" ] && grep -qF "$MARK_BEGIN" "$TMUX_CONF"; then
-    say "binding already present"
+elif ! command -v tmux >/dev/null 2>&1; then
+    say "tmux not installed — the keybinding is unavailable."
+    say "cc-yank still works as a CLI: $REPO/bin/cc-yank"
 else
-    cat >> "$TMUX_CONF" <<EOF
+    # Quote for two parsers: tmux reads a single command argument, then sh
+    # executes that command. A pair of double quotes around the path alone
+    # still expands dollar signs and breaks on embedded quotes.
+    binding=$(python3 - "$REPO/bin/cc-yank" <<'PY'
+import shlex, sys
+command = shlex.quote(sys.argv[1]).replace("#", "##") + " #{pane_id}"
+print("bind-key y run-shell -b " + shlex.quote(command))
+PY
+)
+    if [ -f "$TMUX_CONF" ] && grep -qF "$MARK_BEGIN" "$TMUX_CONF"; then
+        python3 - "$TMUX_CONF" "$binding" <<'PY'
+import os, shutil, sys
+path, binding = sys.argv[1:]
+with open(path) as fh:
+    original = fh.readlines()
+lines = []
+managed = False
+for line in original:
+    if line.rstrip("\n") == "# >>> cc-yank >>>":
+        managed = True
+    elif line.rstrip("\n") == "# <<< cc-yank <<<":
+        managed = False
+    if managed and line.startswith("bind-key y run-shell "):
+        line = binding + "\n"
+    lines.append(line)
+if lines != original:
+    tmp = path + ".tmp"
+    with open(tmp, "w") as fh:
+        fh.writelines(lines)
+    shutil.copymode(path, tmp)
+    os.replace(tmp, path)
+    print("  updated binding quoting")
+else:
+    print("  binding already present")
+PY
+    else
+        cat >> "$TMUX_CONF" <<EOF
 $MARK_BEGIN
 # prefix + y copies Claude Code's last answer. Prefix-based on purpose: a raw
 # binding would swallow the key before Claude Code's TUI ever sees it.
-bind-key y run-shell -b '"$REPO/bin/cc-yank" #{pane_id}'
+$binding
 $MARK_END
 EOF
-    say "added prefix + y binding to $TMUX_CONF"
+        say "added prefix + y binding to $TMUX_CONF"
+    fi
 fi
 
 # set-clipboard drives OSC 52, the only thing that reaches a clipboard over
 # SSH. `on` and `external` both work; only `off` breaks cc-yank.
 if command -v tmux >/dev/null 2>&1 && [ "$uninstall" -eq 0 ]; then
     clip=$(tmux show-options -gv set-clipboard 2>/dev/null || echo external)
     if [ "$clip" = "off" ]; then
-        printf '%s\nset -g set-clipboard external\n%s\n' "$MARK_BEGIN" "$MARK_END" >> "$TMUX_CONF"
-        say "set-clipboard was off — set to external (required for OSC 52)"
+        if ! sed -n "/^$MARK_BEGIN\$/,/^$MARK_END\$/p" "$TMUX_CONF" |
+            grep -qFx 'set -g set-clipboard external'; then
+            printf '%s\nset -g set-clipboard external\n%s\n' "$MARK_BEGIN" "$MARK_END" >> "$TMUX_CONF"
+        fi
+        say "set-clipboard is off — external is configured; reload tmux config to activate"
     else
         say "set-clipboard = $clip (ok)"
     fi
 fi
 
 echo
 if [ "$uninstall" -eq 1 ]; then
-    echo "Uninstalled. Restart Claude Code, and run: tmux kill-server"
+    echo "Uninstalled. Restart Claude Code. In a running tmux, run: tmux unbind-key y"
 else
     cat <<EOF
 Installed. To activate:

tests/test_cli.sh

@@ -8,8 +8,8 @@ set -eu
 # ------------------------------------------------------------------- locate
 # Resolve paths relative to this script, not the caller's cwd (install.sh
 # uses the same CDPATH= cd -- pattern for the same reason).
-SELF_DIR=$(CDPATH= cd -- "$(dirname -- "$0")" && pwd)
-ROOT=$(CDPATH= cd -- "$SELF_DIR/.." && pwd)
+SELF_DIR=$(CDPATH='' cd -- "$(dirname -- "$0")" && pwd)
+ROOT=$(CDPATH='' cd -- "$SELF_DIR/.." && pwd)
 CLI="$ROOT/bin/cc-yank"
 
 TMP=$(mktemp -d)