Remove dead bash hooks after Python port

- Delete the four ported bash hooks from plugins/memory/hooks (now live only in git history; runtime uses the Python ports)
- Update tests/README to reflect removal; test harness drives Python hooks via python-wrappers adapters (preserved)

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

plugins/memory/hooks/post-tool-use-write.sh

@@ -1,55 +0,0 @@
-#!/usr/bin/env bash
-# post-tool-use-write.sh — PostToolUse hook for Write/Edit tool calls
-# Fires after every Write or Edit; updates the Graphify graph if the file
-# is a .md file inside the configured vault.
-
-# Ensure log directory exists
-mkdir -p ~/.cache/graphify
-
-# Parse config with python3+PyYAML; handles missing file, missing key, and tilde
-VAULT_PATH=$(python3 -c '
-import yaml, os
-p = os.path.expanduser("~/.claude/plugins/memory/config.yaml")
-cfg = (yaml.safe_load(open(p)) or {}) if os.path.exists(p) else {}
-print(os.path.expanduser(cfg.get("vault_path", "~/Documents/SecondBrain")))
-')
-
-# Capture stdin
-STDIN=$(cat)
-
-# Extract fields
-FILE_PATH=$(echo "$STDIN" | jq -r '.tool_input.file_path // empty')
-SESSION_ID=$(echo "$STDIN" | jq -r '.session_id // empty')
-
-# Guard: exit silently if FILE_PATH is empty
-if [[ -z "$FILE_PATH" ]]; then
-  exit 0
-fi
-
-# Guard: exit silently if file does not end in .md
-if [[ "$FILE_PATH" != *.md ]]; then
-  exit 0
-fi
-
-# Guard: exit silently if file is not under VAULT_PATH
-if [[ "$FILE_PATH" != "$VAULT_PATH"* ]]; then
-  exit 0
-fi
-
-# Record vault write and invalidate rebuild stamp
-LOG="$HOME/.cache/graphify/post-tool-use.log"
-
-# Always record touched path for session-end reconciliation
-TOUCH_FILE="/tmp/claude-vault-touched-$SESSION_ID"
-echo "$FILE_PATH" >> "$TOUCH_FILE"
-
-# Invalidate the rebuild stamp so next SessionStart triggers an incremental --update rebuild
-STAMP_FILE="$HOME/.cache/graphify/vault-rebuild.stamp"
-if rm -f "$STAMP_FILE"; then
-  echo "[$(date -u +%Y-%m-%dT%H:%M:%SZ)] Invalidated rebuild stamp: $FILE_PATH" >> "$LOG"
-else
-  # Deletion failed (shouldn't happen), but never block
-  echo "[$(date -u +%Y-%m-%dT%H:%M:%SZ)] WARN: Could not delete rebuild stamp for $FILE_PATH" >> "$LOG"
-fi
-
-exit 0

plugins/memory/hooks/session-context.sh

@@ -1,46 +0,0 @@
-#!/usr/bin/env bash
-# UserPromptSubmit hook — injects project graph path on the FIRST user prompt per session.
-# Outputs: {"hookSpecificOutput": {"hookEventName": "UserPromptSubmit", "additionalContext": "..."}}
-# On subsequent prompts: outputs {} (no-op).
-
-# Do NOT set -e — failures are expected and handled.
-
-# ---------------------------------------------------------------------------
-# 0. Read stdin
-# ---------------------------------------------------------------------------
-STDIN_JSON="$(cat 2>/dev/null || true)"
-
-SESSION_ID="$(printf '%s' "$STDIN_JSON" | python3 -c "import sys,json; d=json.load(sys.stdin); print(d.get('session_id','unknown'))" 2>/dev/null || true)"
-CWD="$(printf '%s' "$STDIN_JSON" | python3 -c "import sys,json; d=json.load(sys.stdin); print(d.get('cwd',''))" 2>/dev/null || true)"
-CWD="${CWD:-$PWD}"
-
-FLAG_FILE="/tmp/memory-context-injected-${SESSION_ID:-unknown}"
-
-if [ -f "$FLAG_FILE" ]; then
-    echo '{}'
-    exit 0
-fi
-touch "$FLAG_FILE"
-
-# ---------------------------------------------------------------------------
-# 1. Project graph pointer (only output)
-# ---------------------------------------------------------------------------
-CONTEXT=""
-
-PROJECT_ROOT="$(git -C "$CWD" rev-parse --show-toplevel 2>/dev/null || true)"
-if [ -n "$PROJECT_ROOT" ]; then
-    PROJECT_GRAPH="$PROJECT_ROOT/graphify-out/graph.json"
-    if [ -f "$PROJECT_GRAPH" ]; then
-        CONTEXT="## Project Graph
-
-Project graph: ${PROJECT_GRAPH}
-"
-    fi
-fi
-
-# ---------------------------------------------------------------------------
-# 2. Emit JSON
-# ---------------------------------------------------------------------------
-OUTPUT="$(python3 -c "import json, sys; print(json.dumps({'hookSpecificOutput': {'hookEventName': 'UserPromptSubmit', 'additionalContext': sys.argv[1]}}))" "$CONTEXT" 2>/dev/null)"
-printf '%s\n' "$OUTPUT"
-exit 0

plugins/memory/hooks/session-end.sh

@@ -1,99 +0,0 @@
-#!/usr/bin/env bash
-# session-end.sh — SessionEnd hook
-# Fires at session end; appends a journal entry to the vault's daily log.
-# Exit code is ignored by Claude Code — used for cleanup/logging only.
-
-# Capture stdin
-STDIN=$(cat)
-
-# Extract fields
-SESSION_ID=$(echo "$STDIN" | jq -r '.session_id // empty')
-REASON=$(echo "$STDIN" | jq -r '.reason // empty')
-
-# Guard: if SESSION_ID is empty, use PID as fallback to ensure unique path
-if [ -z "$SESSION_ID" ]; then
-  SESSION_ID="unknown-$$"
-fi
-
-# Parse config with python3+PyYAML; handles missing file, missing key, and tilde
-VAULT_PATH=$(python3 -c '
-import yaml, os
-p = os.path.expanduser("~/.claude/plugins/memory/config.yaml")
-cfg = (yaml.safe_load(open(p)) or {}) if os.path.exists(p) else {}
-print(os.path.expanduser(cfg.get("vault_path", "~/Documents/SecondBrain")))
-')
-
-# Compute journal path
-JOURNAL_DIR="$VAULT_PATH/journal"
-JOURNAL_PATH="$JOURNAL_DIR/$(date -u +%Y-%m-%d).md"
-
-# Ensure journal directory exists
-mkdir -p "$JOURNAL_DIR"
-
-# Create journal note if absent (minimal frontmatter)
-if [[ ! -f "$JOURNAL_PATH" ]]; then
-  cat >"$JOURNAL_PATH" <<'EOF'
----
-summary: Daily session log
-tags: [scope/global, type/log]
----
-EOF
-fi
-
-# Read touched paths from temp file
-TOUCH_FILE="/tmp/claude-vault-touched-$SESSION_ID"
-TOUCHED=$(cat "$TOUCH_FILE" 2>/dev/null || echo "")
-
-# Format touched paths list
-if [[ -z "$TOUCHED" ]]; then
-  TOUCHED_LIST="(none)"
-else
-  TOUCHED_LIST="$TOUCHED"
-fi
-
-# Determine project context
-PROJECT=$(git rev-parse --show-toplevel 2>/dev/null || echo "${CLAUDE_PROJECT_DIR:-unknown}")
-
-# UTC timestamp for entry header
-TIMESTAMP=$(date -u +%Y-%m-%dT%H:%M:%SZ)
-
-# Append journal entry
-{
-  echo ""
-  echo "## Session — $TIMESTAMP"
-  echo ""
-  echo "**Project:** $PROJECT"
-  echo "**Reason:** $REASON"
-  echo "**Vault notes touched:**"
-  echo "$TOUCHED_LIST"
-} >> "$JOURNAL_PATH"
-
-# Cleanup temp file
-rm -f "$TOUCH_FILE"
-
-# ── memsearch memory git sync (fail-safe) ───────────────────────────────────
-# Auto-commit + push the memsearch memory store (~/.memsearch) on session end.
-# We own this sync here so we never patch the marketplace memsearch plugin
-# (which clobbers on update). The whitelist .gitignore in ~/.memsearch tracks
-# only memory/*.md + .gitignore, so `add -A` is safe.
-#
-# Robustness contract: this block MUST NEVER fail session shutdown.
-#   - Skips silently if ~/.memsearch is not a git repo.
-#   - Only commits when something is staged (no empty commits).
-#   - Push is hard-timeboxed and failures are swallowed; the next session's
-#     hook catches up since the daily memory files are append-only.
-# Wrapped in a subshell with `|| true` so nothing here can abort the hook.
-(
-  MEMSEARCH_DIR="/home/jared/.memsearch"
-  if [ -d "$MEMSEARCH_DIR/.git" ]; then
-    git -C "$MEMSEARCH_DIR" add -A >/dev/null 2>&1
-    if ! git -C "$MEMSEARCH_DIR" diff --cached --quiet; then
-      git -C "$MEMSEARCH_DIR" commit -m "memsearch: session memory $(date +%F)" >/dev/null 2>&1
-      echo "[session-end] memsearch memory committed"
-    fi
-    timeout 30 git -C "$MEMSEARCH_DIR" push --quiet origin main >/dev/null 2>&1 || true
-  fi
-) || true
-# ────────────────────────────────────────────────────────────────────────────
-
-exit 0

plugins/memory/hooks/session-start.sh

@@ -1,105 +0,0 @@
-#!/usr/bin/env bash
-# SessionStart hook for the memory plugin.
-# Invoked by Claude Code at the start of every session with JSON on stdin.
-# Must return sub-second; heavy work is detached in the background.
-# Context injection is handled by session-context.sh (UserPromptSubmit hook).
-
-# Never let any individual failure exit the whole script.
-# Do NOT set -e — grep-no-match, graphify errors, etc. are all expected.
-
-# ---------------------------------------------------------------------------
-# 0. Read stdin (ignore errors — fields may be absent on older Claude Code)
-# ---------------------------------------------------------------------------
-STDIN_JSON="$(cat 2>/dev/null || true)"
-HOOK_SOURCE="$(printf '%s' "$STDIN_JSON" | python3 -c "import sys,json; d=json.load(sys.stdin); print(d.get('source','unknown'))" 2>/dev/null || true)"
-echo "[$(date -u +%Y-%m-%dT%H:%M:%SZ)] session-start fired: source=${HOOK_SOURCE:-unknown} cwd=$(pwd)" >> /tmp/memory-hook.log 2>/dev/null || true
-CWD="$(printf '%s' "$STDIN_JSON" | python3 -c "import sys,json; d=json.load(sys.stdin); print(d.get('cwd',''))" 2>/dev/null || true)"
-CWD="${CWD:-$PWD}"
-
-# ---------------------------------------------------------------------------
-# 1. Parse config.yaml — emit shell variable assignments, eval them in.
-#    python3 + PyYAML are guaranteed present via graphify.
-# ---------------------------------------------------------------------------
-eval "$(python3 - <<'PY'
-import yaml, os, shlex, sys
-
-CONFIG_PATH = os.path.expanduser("~/.claude/plugins/memory/config.yaml")
-try:
-    with open(CONFIG_PATH) as f:
-        cfg = yaml.safe_load(f) or {}
-except Exception:
-    cfg = {}
-
-out = {
-    "VAULT_PATH":           os.path.expanduser(cfg.get("vault_path",           "~/Documents/SecondBrain")),
-    "GRAPHIFY_OUTPUT_DIR":  os.path.expanduser(cfg.get("graphify_output_dir",  "~/Documents/SecondBrain/.graphify")),
-    "MODEL":                cfg.get("ollama_model",          "qwen25-coder-7b-16k"),
-    "STALE_DAYS":           str(cfg.get("stale_threshold_days", 7)),
-}
-for k, v in out.items():
-    print(f"{k}={shlex.quote(str(v))}")
-
-# Export env block so the background rebuild process inherits them.
-for k, v in (cfg.get("env") or {}).items():
-    print(f"export {k}={shlex.quote(str(v))}")
-PY
-2>/dev/null || true)"
-
-# Apply fallbacks in case the python3 block produced nothing.
-VAULT_PATH="${VAULT_PATH:-$HOME/Documents/SecondBrain}"
-GRAPHIFY_OUTPUT_DIR="${GRAPHIFY_OUTPUT_DIR:-$HOME/Documents/SecondBrain/.graphify}"
-MODEL="${MODEL:-qwen25-coder-7b-16k}"
-STALE_DAYS="${STALE_DAYS:-7}"
-
-# ---------------------------------------------------------------------------
-# 2. Cache dir + file paths
-# ---------------------------------------------------------------------------
-CACHE_DIR="$HOME/.cache/graphify"
-STAMP="$CACHE_DIR/vault-rebuild.stamp"
-LOCK="$CACHE_DIR/vault-rebuild.lock"
-LOGFILE="$CACHE_DIR/vault-rebuild.log"
-
-mkdir -p "$CACHE_DIR" 2>/dev/null || true
-
-# Export vars needed by the detached bash -c subprocess.
-export VAULT_PATH MODEL STAMP LOCK LOGFILE
-
-# ---------------------------------------------------------------------------
-# 3. Staleness check + detached background rebuild
-# ---------------------------------------------------------------------------
-_needs_rebuild() {
-    [ ! -f "$STAMP" ] && return 0
-    # Use python3 for portable mtime arithmetic (avoids `date -d` vs BSD split).
-    python3 - <<PY 2>/dev/null
-import os, time
-stamp = "$STAMP"
-stale_days = int("$STALE_DAYS")
-try:
-    age_days = (time.time() - os.path.getmtime(stamp)) / 86400
-    exit(0 if age_days > stale_days else 1)
-except Exception:
-    exit(0)
-PY
-}
-
-if _needs_rebuild; then
-    if [ -f "$LOCK" ]; then
-        echo "[memory/session-start] rebuild already running (lock present), skipping" >> "$LOGFILE" 2>/dev/null || true
-        echo "[$(date -u +%Y-%m-%dT%H:%M:%SZ)] session-start: rebuild skipped (lock present)" >> /tmp/memory-hook.log 2>/dev/null || true
-    else
-        # Create lock, then spawn fully detached (no inherited stdin/stdout/stderr).
-        touch "$LOCK" 2>/dev/null || true
-        # shellcheck disable=SC2016
-        nohup bash -c \
-            'graphify extract "$VAULT_PATH" --backend ollama --model "$MODEL" --force \
-                >> "$LOGFILE" 2>&1 \
-                && date > "$STAMP" && rm -f "$LOCK" \
-                || (rm -f "$LOCK"; echo "rebuild failed" >> "$LOGFILE")' \
-            </dev/null >/dev/null 2>&1 &
-        echo "[$(date -u +%Y-%m-%dT%H:%M:%SZ)] session-start: rebuild triggered" >> /tmp/memory-hook.log 2>/dev/null || true
-    fi
-else
-    echo "[$(date -u +%Y-%m-%dT%H:%M:%SZ)] session-start: rebuild not needed" >> /tmp/memory-hook.log 2>/dev/null || true
-fi
-
-exit 0

plugins/memory/tests/README.md

@@ -116,9 +116,12 @@ journal fixture is expected.
 
 ## Running all scenarios
 
+The bash hooks (`hooks/*.sh`) were removed after parity was verified — they live in git
+history only. The only supported invocation uses the Python hooks via `tests/python-wrappers/`:
+
 ```bash
 cd /home/jared/dev/cc-os/plugins/memory/tests
-bash generate-fixtures.sh
+HOOKS_DIR="$(pwd)/python-wrappers" bash generate-fixtures.sh
 ```
 
 The script:
@@ -129,16 +132,19 @@ The script:
 
 ## Replaying against the Python hooks
 
-The Python hooks are now canonical. The bash `.sh` files remain alongside them for reference but are no longer the source of truth. To validate parity (e.g. after modifying a Python hook):
+The Python hooks are canonical. The bash `.sh` files were removed after parity was verified
+(2026-06-12) and exist only in git history. To validate the Python hooks against golden
+fixtures (e.g. after modifying a hook):
 
-1. Ensure each Python hook is executable at a known path (they live in `../hooks/`).
+1. Ensure the Python hooks are executable in `../hooks/` and the wrappers are in
+   `tests/python-wrappers/`.
 
-2. Run generate-fixtures.sh with HOOKS_DIR and --replay-dir overridden:
+2. Run generate-fixtures.sh via python-wrappers with a replay dir:
    ```bash
-   HOOKS_DIR=/path/to/python-hooks \
+   HOOKS_DIR=/home/jared/dev/cc-os/plugins/memory/tests/python-wrappers \
      bash tests/generate-fixtures.sh --replay-dir /tmp/replay-out
    ```
-   This writes new fixtures to `/tmp/replay-out` using the Python hooks instead of bash hooks.
+   This writes new fixtures to `/tmp/replay-out` using the Python hooks.
 
 3. Diff against the committed golden directory:
    ```bash
@@ -156,9 +162,8 @@ since golden fixtures were generated). The before==after safety invariant is alw
 1. **session-start-stale is inherently racy.** The hook spawns graphify via `nohup ... &`
    and exits immediately. The harness polls for the shim log up to 5 seconds. On heavily
    loaded systems the poll may time out; if so, `graphify-shim-args.txt` will say
-   `(graphify not invoked within 5s)` — re-run in that case. This is a known caveat of the
+   `(graphify not invoked within 5s)` — re-run in that case. The Python port uses the same
-   bash design; the Python port should spawn the same detached pattern or document the
+   detached spawn pattern.
-   behavioral difference.
 
 2. **session-start cwd in log lines is normalized to `__CWD__`.** The hook logs
    `cwd=$(pwd)` (shell invocation directory, not the JSON `cwd` field). This varies by