setup.sh merges user hooks instead of overwriting (DPLAN-0234 Strand C). AIPass bridge entries are refreshed on every install (bridges/claude.py marker); user-wired hooks and custom events now survive install/re-run. Fixture-verified: customs preserved, stale bridge entries replaced without duplicates, fresh-install output shape-identical (7 events, 6+6 entries). Background: full hook fire-test on fresh Linux Docker install passed 17/17.

CHANGELOG.md

@@ -11,6 +11,37 @@ PyPI version — not the changelog header.
 
 ## [2026-07-05]
 
+### Fixed
+
+- **HVTrust badge restored in the root README.** hvtracker corrected the
+  methodology v4.1 grade-computation bug (issue #109); the badge shows the
+  right grade again, so the temporary comment-out from earlier today is
+  reverted.
+
+- **Installer no longer destroys a user's custom Claude Code hooks (DPLAN-0234
+  Strand C).** setup.sh used to write `settings["hooks"]` wholesale — anyone
+  with their own hooks in `~/.claude/settings.json` lost them on install or
+  re-run. Now it merges: every AIPass bridge entry (identified by the
+  `bridges/claude.py` marker) is refreshed, while user-wired hooks and custom
+  events are preserved. Verified against fixtures: custom hooks survive, stale
+  AIPass entries are replaced without duplicates, and the fresh-install output
+  is shape-identical to before (7 events, 6 UserPromptSubmit + 6 PreCompact
+  entries). Found while fire-testing a fresh install's hooks in Docker — all
+  17 wired hook entries pass on a cold Linux clone (real kernel/navmap/branch
+  prompt bytes, git gate blocks, clean no-ops on empty state).
+
+- **Windows fresh installs get a working hook bridge.** setup.sh wrote the
+  Claude bridge command with `.venv/bin/python3` on every OS — but Windows
+  venvs put the interpreter at `.venv/Scripts/python.exe` and have no `bin/`,
+  so hooks on a fresh Windows install pointed at a nonexistent python and
+  would never fire. The bridge string is now OS-aware (bash passes
+  `IS_WINDOWS` into the hook-install step). @hooks assessed the rest of the
+  chain: `$AIPASS_HOME` expansion works on Windows because Claude Code runs
+  hooks via Git Bash (which must exist for setup.sh to have run), and the
+  bridge itself has zero POSIX assumptions — the interpreter path was the
+  only gap. Verified: both OS modes produce the right bridge string, merge
+  marker unchanged, custom-hook preservation intact. (assessed by @hooks)
+
 ### Added
 
 - **`./aipass` — repo-root cold-clone launcher (DPLAN-0234 Strand B).** The

CONTRIBUTING.md

@@ -15,7 +15,7 @@ PRs are welcome after an issue has been discussed. Keep changes focused -- one f
 - Python 3.10+
 - Tests: `pytest` (4,900+ tests across the project)
 - Quality: AIPass uses its own standards system ([seedgo](src/aipass/seedgo/README.md)) for automated audits
-- Run `./setup.sh` to bootstrap the full environment
+- Run `./aipass install --no-init` to bootstrap the full environment (contributors work in the engine repo itself — no first-project scaffold needed)
 
 ## Questions?
 

README.md

@@ -5,8 +5,7 @@
 [![codecov](https://codecov.io/gh/AIOSAI/AIPass/graph/badge.svg)](https://codecov.io/gh/AIOSAI/AIPass)
 [![OpenSSF Scorecard](https://api.scorecard.dev/projects/github.com/AIOSAI/AIPass/badge)](https://scorecard.dev/viewer/?uri=github.com/AIOSAI/AIPass)
 [![OpenSSF Best Practices](https://www.bestpractices.dev/projects/13095/badge)](https://www.bestpractices.dev/projects/13095)
-<!-- HVTrust badge temporarily hidden 2026-07-05: hvtracker methodology v4.1 recalibration bug is showing Grade D/~10 (dimensions on the detail page sum to ~78); correction filed as hvtracker issue #109. Restore when resolved. Was:
-[![HVTrust](https://hvtracker.net/badge/aipass.svg)](https://hvtracker.net/agents/aipass) -->
+[![HVTrust](https://hvtracker.net/badge/aipass.svg)](https://hvtracker.net/agents/aipass)
 
 <p align="center">
   <img src="assets/logo.png" alt="AIPass" width="400" />
@@ -232,7 +231,7 @@ AIPass is built and tested with **Claude Code** on Linux/WSL.
 | [Claude Code](https://code.claude.com/docs) | `claude -p "prompt" --permission-mode bypassPermissions` | Fully tested |
 | [Codex](https://github.com/openai/codex) | `codex exec "prompt" --dangerously-bypass-approvals-and-sandbox` | Experimental |
 
-setup.sh auto-detects which CLIs are installed and configures hooks for each.
+The installer (`./aipass install`, powered by setup.sh) auto-detects which CLIs are installed and configures hooks for each — merging with any hooks you've already wired, never overwriting them.
 
 ---
 

setup.sh

@@ -633,19 +633,24 @@ if [ -f "$SCRIPT_DIR/src/aipass/hooks/apps/handlers/bridges/claude.py" ]; then
     echo "Installing Claude Code hooks ..."
     mkdir -p "$HOME/.claude"
 
-    "$PYTHON" - "$SCRIPT_DIR" "$CLAUDE_SETTINGS" << 'PYEOF'
+    "$PYTHON" - "$SCRIPT_DIR" "$CLAUDE_SETTINGS" "$IS_WINDOWS" << 'PYEOF'
 import json
 import os
 import sys
 from pathlib import Path
 
 repo_root = sys.argv[1]
 settings_path = Path(sys.argv[2])
+is_windows = len(sys.argv) > 3 and sys.argv[3] == "1"
 
 # Bridge entry point — all hooks route through the engine via this bridge.
 # Uses $AIPASS_HOME env var (injected into settings.env below) so the
-# settings file stays relocatable.
-bridge = "$AIPASS_HOME/.venv/bin/python3 $AIPASS_HOME/src/aipass/hooks/apps/handlers/bridges/claude.py"
+# settings file stays relocatable. CC on Windows runs hooks via Git Bash
+# (which must exist for setup.sh to have run), so $VAR expansion works —
+# but the venv interpreter lives at Scripts/python.exe there, not bin/python3
+# (@hooks assessment, DPLAN-0234 Strand C).
+venv_python = ".venv/Scripts/python.exe" if is_windows else ".venv/bin/python3"
+bridge = f"$AIPASS_HOME/{venv_python} $AIPASS_HOME/src/aipass/hooks/apps/handlers/bridges/claude.py"
 
 # Load existing settings or start fresh
 if settings_path.exists():
@@ -657,7 +662,7 @@ else:
 # UserPromptSubmit: 5 separate entries (EventType:hook_name) to avoid output merging
 # PreToolUse, PostToolUse, SubagentStop, Stop, Notification: single aggregate entries
 # PreCompact: 3 hooks x 2 matchers (manual + auto) = 6 entries
-settings["hooks"] = {
+aipass_hooks = {
     "UserPromptSubmit": [
         {"hooks": [{"type": "command", "command": f"{bridge} UserPromptSubmit:tier0_kernel"}]},
         {"hooks": [{"type": "command", "command": f"{bridge} UserPromptSubmit:navmap"}]},
@@ -693,6 +698,19 @@ settings["hooks"] = {
     ],
 }
 
+# Merge, don't replace (DPLAN-0234 Strand C): refresh every AIPass bridge entry
+# (identified by the bridges/claude.py marker) but preserve any hooks the user
+# wired themselves. Re-runs stay idempotent; custom hooks survive reinstall.
+existing_hooks = settings.get("hooks", {})
+merged_hooks = {}
+for event in set(existing_hooks) | set(aipass_hooks):
+    user_entries = [
+        entry for entry in existing_hooks.get(event, [])
+        if "bridges/claude.py" not in json.dumps(entry)
+    ]
+    merged_hooks[event] = aipass_hooks.get(event, []) + user_entries
+settings["hooks"] = merged_hooks
+
 # Inject AIPASS_HOME into env block so dispatched agents find AIPass
 env_block = settings.get("env", {})
 env_block["AIPASS_HOME"] = repo_root