fix(install): respect $CLAUDE_CONFIG_DIR in install/uninstall/update

[halindrome]

Summary

codebase-memory-mcp install (and therefore update's Step 6 refresh) hardcoded $HOME/.claude/... for skills, MCP entries, hook scripts, .claude.json, and settings.json. When users had CLAUDE_CONFIG_DIR set to a non-default location (e.g. ~/.config/claude-code, where Claude Code's own config lives), the installer silently created a separate ~/.claude/ tree that the agent never saw. Hooks installed at runtime already honored CLAUDE_CONFIG_DIR; only the install/uninstall paths were mismatched.

This PR fixes that. It also bundles a migration nudge so the same release that fixes the bug helps users with stale ~/.claude/ trees clean them up — explained under "Bundling rationale" below.

Closes #320.

What changes

Core helpers in src/cli/cli.c:

• cbm_claude_config_dir(home, out, sz) — returns $CLAUDE_CONFIG_DIR or $home/.claude.
• cbm_claude_user_root(home, out, sz) — returns $CLAUDE_CONFIG_DIR or $home (parent dir for .claude.json, which moves to $CLAUDE_CONFIG_DIR/.claude.json when the env var is set, matching Claude Code's own behavior).
• cbm_resolve_hook_command(script_name, out, sz) — produces the hook command string written into settings.json. When CLAUDE_CONFIG_DIR is unset, it preserves the legacy ~/.claude/hooks/<script> tilde form so existing settings.json files stay portable across HOME values.

Call sites routed through the helpers:

• install_claude_code_config — skills, .mcp.json, .claude.json, settings.json, hook script install
• uninstall_claude_code — same set, mirrored
• cbm_install_hook_gate_script, cbm_install_session_reminder_script — hook script destination
• cbm_detect_agents — agents.claude_code now true when either ~/.claude or $CLAUDE_CONFIG_DIR exists

The CMM_HOOK_COMMAND / CMM_SESSION_COMMAND macros (which baked ~/.claude/hooks/... into settings.json) are replaced by CMM_HOOK_GATE_SCRIPT / CMM_SESSION_REMINDER_SCRIPT (basenames), with the full path resolved at install time via cbm_resolve_hook_command. Removal still works because is_cmm_hook_entry matches by matcher_str, not by command path.

Shell layer:

• scripts/setup.sh — configure_claude now uses ${CLAUDE_CONFIG_DIR:-$HOME/.claude} for settings_file and the printed instructions.
• scripts/security-install.sh — SKILLS_DIR likewise.

Bundling rationale

This PR rolls out the fix and the migration nudge together rather than splitting them across two releases:

• If we shipped only the fix, users who upgrade with CLAUDE_CONFIG_DIR set would see their config silently migrate to the env-pointed dir. Their old ~/.claude/{skills,hooks,settings.json,.mcp.json} would still be on disk — orphaned, never written again, easy to forget.
• The migration nudge is a single stderr line printed by install when (a) CLAUDE_CONFIG_DIR is set, and (b) a legacy ~/.claude directory still exists. It names both paths so users can choose to clean up.
• Shipping them together means the user sees the corrective behavior and the cleanup hint in the same release. Splitting them would force a two-release rollout where the first release leaves stale state on disk with no in-product signal, and the second release shows up later when many users would have already noticed and worked around it.

The nudge is non-fatal, prints once per install invocation, and is silent in the legacy-default case (CLAUDE_CONFIG_DIR unset → no divergence to nudge about).

Tests

• tests/test_cli.c: new cli_detect_agents_finds_claude_via_env asserts that cbm_detect_agents reports claude_code=true when CLAUDE_CONFIG_DIR points at an existing dir outside home_dir/.claude. cli_detect_agents_finds_claude and cli_detect_agents_none_found now unset/restore CLAUDE_CONFIG_DIR so the runner's real env does not leak in. All 2813 unit tests pass.
• scripts/smoke-test.sh Phase 9c: end-to-end install/uninstall under CLAUDE_CONFIG_DIR=$FAKE_HOME/custom-claude with a pre-existing $FAKE_HOME/.claude. Asserts:
  • skills/, settings.json, .mcp.json, .claude.json, hooks/cbm-code-discovery-gate all land under $CLAUDE_CONFIG_DIR.
  • None of those land under $HOME/.claude (regression guard).
  • Hook command in settings.json is the absolute $CLAUDE_CONFIG_DIR/hooks/... path, not ~/.claude/hooks/....
  • Migration nudge fires when both dirs are present.
  • Uninstall removes from $CLAUDE_CONFIG_DIR and leaves legacy $HOME/.claude untouched.
  • With CLAUDE_CONFIG_DIR unset, settings.json keeps the ~/.claude/hooks/... tilde form (legacy default preserved).
• Local manual verification: install + uninstall cycle with both env-set and env-unset configs, confirmed file placement and migration nudge surface match expectations.

Out of scope (intentionally separate)

• Project-local install (--scope=project): a real feature gap, but a separate change. Not bundled.
• The wider EXPECTED_PATTERNS allow-list in scripts/security-install.sh is unchanged; .config/... already matches typical CLAUDE_CONFIG_DIR setups, and broadening it without a concrete test is not worth the security audit risk.

Test plan

• scripts/build.sh
• scripts/test.sh (2813 passed)
• Manual install/uninstall with CLAUDE_CONFIG_DIR set
• Manual install/uninstall with CLAUDE_CONFIG_DIR unset (legacy default)
• CI: _lint.yml (clang-format-20)
• CI: _build.yml
• CI: smoke-test (full Phase 1-15 including new Phase 9c)

🤖 Generated with Claude Code

[halindrome]

QA Round 1 — PR #321 (fix/claude-config-dir-respect)

Reviewer: QA agent
Branch: halindrome:fix/claude-config-dir-respect → DeusData:main
Diff scope: src/cli/cli.c, tests/test_cli.c, scripts/{setup,security-install,smoke-test}.sh (+311/-25)

Per-check verdict

#	What	Status	Evidence / Notes
1	Helper trio correct (buffer size handling, NULL guards, env precedence, tilde preserved only when env unset)	PASS	All three helpers (cbm_claude_config_dir, cbm_claude_user_root, cbm_resolve_hook_command) early-return on out_sz==0, zero-init out[0]='\0', branch on cbm_safe_getenv (non-empty wins) then fall back to home_dir. cbm_resolve_hook_command emits ~/.claude/hooks/<name> only when env unset.
2	Every ~/.claude/... write site routed through helpers	PASS	Remaining literals in src/cli/cli.c: lines 973/984/988/1017 (helper bodies), 1692 (comment), 2715/2736/3048 (paths derived from home-based legacy_dir/mcp_path2/comment — all correct uses). cli.h lines 67/113/168 are doc comments. No missed callsite.
3	.claude.json placement: $CCD/.claude.json when env set, else $HOME/.claude.json	PASS	cbm_claude_user_root returns env-or-home; mcp_path2 is <user_root>/.claude.json in both install_claude_code_config (line 2715) and uninstall_claude_code (line 3048). Manual T1 confirms .claude.json written under $CCD, no stray $HOME/.claude.json.
4	Hook command in settings.json: tilde when env unset, absolute when env set	PASS	Manual T1: PreToolUse: $CCD/hooks/cbm-code-discovery-gate; SessionStart: $CCD/hooks/cbm-session-reminder. Manual T2 (env unset): PreToolUse: ~/.claude/hooks/cbm-code-discovery-gate; SessionStart: ~/.claude/hooks/cbm-session-reminder.
5	Removal symmetry — old ~/.claude/... entries replaced by env-set absolute path	PASS	is_cmm_hook_entry matches by matcher_str only (line 1525). Manual T5: installed with env unset (1 PreToolUse entry, tilde cmd) → re-installed with CCD set → settings.json still has 1 PreToolUse entry, command rewritten to absolute path. SessionStart: still exactly 4 entries, all rewritten.
6	Migration nudge condition (CCD set AND legacy exists AND differs); no false positives	PASS	T1 (CCD set, legacy present, differs): nudge fires. T2 (CCD unset): silent. T3 (CCD set, no legacy dir): silent. T4 (CCD == $HOME/.claude): silent (the strcmp(legacy_dir, config_dir) != 0 guard handles the identical-path case).
7	Test coverage matches PR claims	PASS	New cli_detect_agents_finds_claude_via_env exercises env-set path with no home/.claude. Existing cli_detect_agents_finds_claude and cli_detect_agents_none_found now save/restore CLAUDE_CONFIG_DIR so the runner's real env can't leak. Phase 9c covers 10 placement/nudge/uninstall/symmetry assertions.
8	Shell layer minimal & correct	PASS	setup.sh swaps the literal for ${CLAUDE_CONFIG_DIR:-$HOME/.claude} plus updates the printed instruction text. security-install.sh swaps SKILLS_DIR. Both use the standard :- fallback idiom. No accidental side effects.
9	Style — conventional commits, code style consistent, no debug prints, no leftover TODO	PASS	All commits follow fix({scope}) pattern. Helpers follow the file's static-helper / snprintf / CLI_BUF_1K conventions. No printf debug prints. No // TODO.
10	Backwards compatibility — pre-existing settings.json with ~/.claude/hooks/... upserts cleanly	PASS	T5 confirmed matcher-based dedup: only one PreToolUse entry survives the env-flip upgrade, with the command rewritten to the new absolute form.
11	Full test suite	PASS	scripts/test.sh: 2813 passed, 0 failed.

Findings

Must-fix: None.

Nice-to-have (advisory only):

1. Doc comment drift. src/cli/cli.c:1692 and src/cli/cli.h:{67,113,168} still describe paths as ~/.claude/... even though install location is now CCD-aware. Comments are not load-bearing for behavior, but a one-line update to mention "or $CLAUDE_CONFIG_DIR" would prevent future grep confusion.
2. Migration nudge wording. The current nudge prints the absolute legacy path (e.g. legacy /tmp/x/.claude still exists). If the user invoked install from a non-interactive context the absolute path is fine; for interactive use, ~/.claude reads more cleanly. Strictly cosmetic.
3. config_dir[0]==0 guard divergence. cbm_install_hook_gate_script and cbm_install_session_reminder_script early-return when config_dir[0] is empty, but install_claude_code_config itself does not check config_dir[0] before deriving skills_dir/mcp_path/settings_path. In practice home==NULL is already filtered upstream, so this is unreachable, but adding a symmetric if (!config_dir[0]) return; would be defensive.
4. cli.h cbm_detected_agents_t.claude_code comment still says /* ~/.claude/ exists */; could read /* ~/.claude or $CLAUDE_CONFIG_DIR exists */ to match the new detection semantics.

No security or correctness regression detected.

Final verdict

PASS-WITH-ADVISORY — the fix is correct, well-tested, and backwards-compatible. The four advisory items are documentation-comment polish, not behavior bugs. Recommend marking the PR ready for review.