fix: resolve 9 CLI and config bugs (#734, #737, #739, #740, #741, #759, #786, #664, #670)

agents/gsd-debugger.md

@@ -1027,7 +1027,7 @@ mv .planning/debug/{slug}.md .planning/debug/resolved/
 **Check planning config using state load (commit_docs is available from the output):**
 
 ```bash
-INIT=$(node ~/.claude/get-shit-done/bin/gsd-tools.cjs state load)
+INIT=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" state load)
 # commit_docs is in the JSON output
 ```
 
@@ -1044,7 +1044,7 @@ Root cause: {root_cause}"
 
 Then commit planning docs via CLI (respects `commit_docs` config automatically):
 ```bash
-node ~/.claude/get-shit-done/bin/gsd-tools.cjs commit "docs: resolve debug {slug}" --files .planning/debug/resolved/{slug}.md
+node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" commit "docs: resolve debug {slug}" --files .planning/debug/resolved/{slug}.md
 ```
 
 Report completion and offer next steps.

agents/gsd-executor.md

@@ -21,7 +21,7 @@ Before executing, discover project context:
 
 **Project instructions:** Read `./CLAUDE.md` if it exists in the working directory. Follow all project-specific guidelines, security requirements, and coding conventions.
 
-**Project skills:** Check `.agents/skills/` directory if it exists:
+**Project skills:** Check `.claude/skills/` or `.agents/skills/` directory if either exists:
 1. List available skills (subdirectories)
 2. Read `SKILL.md` for each skill (lightweight index ~130 lines)
 3. Load specific `rules/*.md` files as needed during implementation
@@ -37,7 +37,7 @@ This ensures project-specific patterns, conventions, and best practices are appl
 Load execution context:
 
 ```bash
-INIT=$(node ~/.claude/get-shit-done/bin/gsd-tools.cjs init execute-phase "${PHASE}")
+INIT=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" init execute-phase "${PHASE}")
 ```
 
 Extract from init JSON: `executor_model`, `commit_docs`, `phase_dir`, `plans`, `incomplete_plans`.
@@ -190,7 +190,7 @@ Track auto-fix attempts per task. After 3 auto-fix attempts on a single task:
 Check if auto mode is active at executor start:
 
 ```bash
-AUTO_CFG=$(node ~/.claude/get-shit-done/bin/gsd-tools.cjs config-get workflow.auto_advance 2>/dev/null || echo "false")
+AUTO_CFG=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" config-get workflow.auto_advance 2>/dev/null || echo "false")
 ```
 
 Store the result for checkpoint handling below.
@@ -379,34 +379,34 @@ After SUMMARY.md, update STATE.md using gsd-tools:
 
 ```bash
 # Advance plan counter (handles edge cases automatically)
-node ~/.claude/get-shit-done/bin/gsd-tools.cjs state advance-plan
+node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" state advance-plan
 
 # Recalculate progress bar from disk state
-node ~/.claude/get-shit-done/bin/gsd-tools.cjs state update-progress
+node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" state update-progress
 
 # Record execution metrics
-node ~/.claude/get-shit-done/bin/gsd-tools.cjs state record-metric \
+node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" state record-metric \
   --phase "${PHASE}" --plan "${PLAN}" --duration "${DURATION}" \
   --tasks "${TASK_COUNT}" --files "${FILE_COUNT}"
 
 # Add decisions (extract from SUMMARY.md key-decisions)
 for decision in "${DECISIONS[@]}"; do
-  node ~/.claude/get-shit-done/bin/gsd-tools.cjs state add-decision \
+  node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" state add-decision \
     --phase "${PHASE}" --summary "${decision}"
 done
 
 # Update session info
-node ~/.claude/get-shit-done/bin/gsd-tools.cjs state record-session \
+node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" state record-session \
   --stopped-at "Completed ${PHASE}-${PLAN}-PLAN.md"
 ```
 
 ```bash
 # Update ROADMAP.md progress for this phase (plan counts, status)
-node ~/.claude/get-shit-done/bin/gsd-tools.cjs roadmap update-plan-progress "${PHASE_NUMBER}"
+node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" roadmap update-plan-progress "${PHASE_NUMBER}"
 
 # Mark completed requirements from PLAN.md frontmatter
 # Extract the `requirements` array from the plan's frontmatter, then mark each complete
-node ~/.claude/get-shit-done/bin/gsd-tools.cjs requirements mark-complete ${REQ_IDS}
+node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" requirements mark-complete ${REQ_IDS}
 ```
 
 **Requirement IDs:** Extract from the PLAN.md frontmatter `requirements:` field (e.g., `requirements: [AUTH-01, AUTH-02]`). Pass all IDs to `requirements mark-complete`. If the plan has no requirements field, skip this step.
@@ -424,13 +424,13 @@ node ~/.claude/get-shit-done/bin/gsd-tools.cjs requirements mark-complete ${REQ_
 
 **For blockers found during execution:**
 ```bash
-node ~/.claude/get-shit-done/bin/gsd-tools.cjs state add-blocker "Blocker description"
+node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" state add-blocker "Blocker description"
 ```
 </state_updates>
 
 <final_commit>
 ```bash
-node ~/.claude/get-shit-done/bin/gsd-tools.cjs commit "docs({phase}-{plan}): complete [plan-name] plan" --files .planning/phases/XX-name/{phase}-{plan}-SUMMARY.md .planning/STATE.md .planning/ROADMAP.md .planning/REQUIREMENTS.md
+node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" commit "docs({phase}-{plan}): complete [plan-name] plan" --files .planning/phases/XX-name/{phase}-{plan}-SUMMARY.md .planning/STATE.md .planning/ROADMAP.md .planning/REQUIREMENTS.md
 ```
 
 Separate from per-task commits — captures execution results only.

agents/gsd-phase-researcher.md

@@ -26,7 +26,7 @@ Before researching, discover project context:
 
 **Project instructions:** Read `./CLAUDE.md` if it exists in the working directory. Follow all project-specific guidelines, security requirements, and coding conventions.
 
-**Project skills:** Check `.agents/skills/` directory if it exists:
+**Project skills:** Check `.claude/skills/` or `.agents/skills/` directory if either exists:
 1. List available skills (subdirectories)
 2. Read `SKILL.md` for each skill (lightweight index ~130 lines)
 3. Load specific `rules/*.md` files as needed during research
@@ -120,7 +120,7 @@ When researching "best library for X": find what the ecosystem actually uses, do
 Check `brave_search` from init context. If `true`, use Brave Search for higher quality results:
 
 ```bash
-node ~/.claude/get-shit-done/bin/gsd-tools.cjs websearch "your query" --limit 10
+node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" websearch "your query" --limit 10
 ```
 
 **Options:**
@@ -359,7 +359,7 @@ Orchestrator provides: phase number/name, description/goal, requirements, constr
 
 Load phase context using init command:
 ```bash
-INIT=$(node ~/.claude/get-shit-done/bin/gsd-tools.cjs init phase-op "${PHASE}")
+INIT=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" init phase-op "${PHASE}")
 ```
 
 Extract from init JSON: `phase_dir`, `padded_phase`, `phase_number`, `commit_docs`.
@@ -461,7 +461,7 @@ Write to: `$PHASE_DIR/$PADDED_PHASE-RESEARCH.md`
 ## Step 7: Commit Research (optional)
 
 ```bash
-node ~/.claude/get-shit-done/bin/gsd-tools.cjs commit "docs($PHASE): research phase domain" --files "$PHASE_DIR/$PADDED_PHASE-RESEARCH.md"
+node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" commit "docs($PHASE): research phase domain" --files "$PHASE_DIR/$PADDED_PHASE-RESEARCH.md"
 ```
 
 ## Step 8: Return Structured Result

agents/gsd-plan-checker.md

@@ -31,7 +31,7 @@ Before verifying, discover project context:
 
 **Project instructions:** Read `./CLAUDE.md` if it exists in the working directory. Follow all project-specific guidelines, security requirements, and coding conventions.
 
-**Project skills:** Check `.agents/skills/` directory if it exists:
+**Project skills:** Check `.claude/skills/` or `.agents/skills/` directory if either exists:
 1. List available skills (subdirectories)
 2. Read `SKILL.md` for each skill (lightweight index ~130 lines)
 3. Load specific `rules/*.md` files as needed during verification
@@ -365,7 +365,7 @@ If FAIL: return to planner with specific fixes. Same revision loop as other dime
 
 Load phase operation context:
 ```bash
-INIT=$(node ~/.claude/get-shit-done/bin/gsd-tools.cjs init phase-op "${PHASE_ARG}")
+INIT=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" init phase-op "${PHASE_ARG}")
 ```
 
 Extract from init JSON: `phase_dir`, `phase_number`, `has_plans`, `plan_count`.
@@ -376,7 +376,7 @@ Orchestrator provides CONTEXT.md content in the verification prompt. If provided
 ls "$phase_dir"/*-PLAN.md 2>/dev/null
 # Read research for Nyquist validation data
 cat "$phase_dir"/*-RESEARCH.md 2>/dev/null
-node ~/.claude/get-shit-done/bin/gsd-tools.cjs roadmap get-phase "$phase_number"
+node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" roadmap get-phase "$phase_number"
 ls "$phase_dir"/*-BRIEF.md 2>/dev/null
 ```
 
@@ -389,7 +389,7 @@ Use gsd-tools to validate plan structure:
 ```bash
 for plan in "$PHASE_DIR"/*-PLAN.md; do
   echo "=== $plan ==="
-  PLAN_STRUCTURE=$(node ~/.claude/get-shit-done/bin/gsd-tools.cjs verify plan-structure "$plan")
+  PLAN_STRUCTURE=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" verify plan-structure "$plan")
   echo "$PLAN_STRUCTURE"
 done
 ```
@@ -407,7 +407,7 @@ Map errors/warnings to verification dimensions:
 Extract must_haves from each plan using gsd-tools:
 
 ```bash
-MUST_HAVES=$(node ~/.claude/get-shit-done/bin/gsd-tools.cjs frontmatter get "$PLAN_PATH" --field must_haves)
+MUST_HAVES=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" frontmatter get "$PLAN_PATH" --field must_haves)
 ```
 
 Returns JSON: `{ truths: [...], artifacts: [...], key_links: [...] }`
@@ -450,7 +450,7 @@ For each requirement: find covering task(s), verify action is specific, flag gap
 Use gsd-tools plan-structure verification (already run in Step 2):
 
 ```bash
-PLAN_STRUCTURE=$(node ~/.claude/get-shit-done/bin/gsd-tools.cjs verify plan-structure "$PLAN_PATH")
+PLAN_STRUCTURE=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" verify plan-structure "$PLAN_PATH")
 ```
 
 The `tasks` array in the result shows each task's completeness:

agents/gsd-planner.md

@@ -33,7 +33,7 @@ Before planning, discover project context:
 
 **Project instructions:** Read `./CLAUDE.md` if it exists in the working directory. Follow all project-specific guidelines, security requirements, and coding conventions.
 
-**Project skills:** Check `.agents/skills/` directory if it exists:
+**Project skills:** Check `.claude/skills/` or `.agents/skills/` directory if either exists:
 1. List available skills (subdirectories)
 2. Read `SKILL.md` for each skill (lightweight index ~130 lines)
 3. Load specific `rules/*.md` files as needed during planning
@@ -900,7 +900,7 @@ Group by plan, dimension, severity.
 ### Step 6: Commit
 
 ```bash
-node ~/.claude/get-shit-done/bin/gsd-tools.cjs commit "fix($PHASE): revise plans based on checker feedback" --files .planning/phases/$PHASE-*/$PHASE-*-PLAN.md
+node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" commit "fix($PHASE): revise plans based on checker feedback" --files .planning/phases/$PHASE-*/$PHASE-*-PLAN.md
 ```
 
 ### Step 7: Return Revision Summary
@@ -939,7 +939,7 @@ node ~/.claude/get-shit-done/bin/gsd-tools.cjs commit "fix($PHASE): revise plans
 Load planning context:
 
 ```bash
-INIT=$(node ~/.claude/get-shit-done/bin/gsd-tools.cjs init plan-phase "${PHASE}")
+INIT=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" init plan-phase "${PHASE}")
 ```
 
 Extract from init JSON: `planner_model`, `researcher_model`, `checker_model`, `commit_docs`, `research_enabled`, `phase_dir`, `phase_number`, `has_research`, `has_context`.
@@ -995,7 +995,7 @@ Apply discovery level protocol (see discovery_levels section).
 
 **Step 1 — Generate digest index:**
 ```bash
-node ~/.claude/get-shit-done/bin/gsd-tools.cjs history-digest
+node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" history-digest
 ```
 
 **Step 2 — Select relevant phases (typically 2-4):**
@@ -1123,7 +1123,7 @@ Include all frontmatter fields.
 Validate each created PLAN.md using gsd-tools:
 
 ```bash
-VALID=$(node ~/.claude/get-shit-done/bin/gsd-tools.cjs frontmatter validate "$PLAN_PATH" --schema plan)
+VALID=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" frontmatter validate "$PLAN_PATH" --schema plan)
 ```
 
 Returns JSON: `{ valid, missing, present, schema }`
@@ -1136,7 +1136,7 @@ Required plan frontmatter fields:
 Also validate plan structure:
 
 ```bash
-STRUCTURE=$(node ~/.claude/get-shit-done/bin/gsd-tools.cjs verify plan-structure "$PLAN_PATH")
+STRUCTURE=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" verify plan-structure "$PLAN_PATH")
 ```
 
 Returns JSON: `{ valid, errors, warnings, task_count, tasks }`
@@ -1173,7 +1173,7 @@ Plans:
 
 <step name="git_commit">
 ```bash
-node ~/.claude/get-shit-done/bin/gsd-tools.cjs commit "docs($PHASE): create phase plan" --files .planning/phases/$PHASE-*/$PHASE-*-PLAN.md .planning/ROADMAP.md
+node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" commit "docs($PHASE): create phase plan" --files .planning/phases/$PHASE-*/$PHASE-*-PLAN.md .planning/ROADMAP.md
 ```
 </step>
 

agents/gsd-project-researcher.md

@@ -99,7 +99,7 @@ Always include current year. Use multiple query variations. Mark WebSearch-only
 Check `brave_search` from orchestrator context. If `true`, use Brave Search for higher quality results:
 
 ```bash
-node ~/.claude/get-shit-done/bin/gsd-tools.cjs websearch "your query" --limit 10
+node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" websearch "your query" --limit 10
 ```
 
 **Options:**

agents/gsd-research-synthesizer.md

@@ -131,7 +131,7 @@ Write to `.planning/research/SUMMARY.md`
 The 4 parallel researcher agents write files but do NOT commit. You commit everything together.
 
 ```bash
-node ~/.claude/get-shit-done/bin/gsd-tools.cjs commit "docs: complete project research" --files .planning/research/
+node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" commit "docs: complete project research" --files .planning/research/
 ```
 
 ## Step 8: Return Summary

agents/gsd-verifier.md

@@ -21,7 +21,7 @@ Before verifying, discover project context:
 
 **Project instructions:** Read `./CLAUDE.md` if it exists in the working directory. Follow all project-specific guidelines, security requirements, and coding conventions.
 
-**Project skills:** Check `.agents/skills/` directory if it exists:
+**Project skills:** Check `.claude/skills/` or `.agents/skills/` directory if either exists:
 1. List available skills (subdirectories)
 2. Read `SKILL.md` for each skill (lightweight index ~130 lines)
 3. Load specific `rules/*.md` files as needed during verification
@@ -72,7 +72,7 @@ Set `is_re_verification = false`, proceed with Step 1.
 ```bash
 ls "$PHASE_DIR"/*-PLAN.md 2>/dev/null
 ls "$PHASE_DIR"/*-SUMMARY.md 2>/dev/null
-node ~/.claude/get-shit-done/bin/gsd-tools.cjs roadmap get-phase "$PHASE_NUM"
+node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" roadmap get-phase "$PHASE_NUM"
 grep -E "^| $PHASE_NUM" .planning/REQUIREMENTS.md 2>/dev/null
 ```
 
@@ -109,7 +109,7 @@ must_haves:
 If no must_haves in frontmatter, check for Success Criteria:
 
 ```bash
-PHASE_DATA=$(node ~/.claude/get-shit-done/bin/gsd-tools.cjs roadmap get-phase "$PHASE_NUM" --raw)
+PHASE_DATA=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" roadmap get-phase "$PHASE_NUM" --raw)
 ```
 
 Parse the `success_criteria` array from the JSON output. If non-empty:
@@ -152,7 +152,7 @@ For each truth:
 Use gsd-tools for artifact verification against must_haves in PLAN frontmatter:
 
 ```bash
-ARTIFACT_RESULT=$(node ~/.claude/get-shit-done/bin/gsd-tools.cjs verify artifacts "$PLAN_PATH")
+ARTIFACT_RESULT=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" verify artifacts "$PLAN_PATH")
 ```
 
 Parse JSON result: `{ all_passed, passed, total, artifacts: [{path, exists, issues, passed}] }`
@@ -201,7 +201,7 @@ Key links are critical connections. If broken, the goal fails even with all arti
 Use gsd-tools for key link verification against must_haves in PLAN frontmatter:
 
 ```bash
-LINKS_RESULT=$(node ~/.claude/get-shit-done/bin/gsd-tools.cjs verify key-links "$PLAN_PATH")
+LINKS_RESULT=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" verify key-links "$PLAN_PATH")
 ```
 
 Parse JSON result: `{ all_verified, verified, total, links: [{from, to, via, verified, detail}] }`
@@ -283,12 +283,12 @@ Identify files modified in this phase from SUMMARY.md key-files section, or extr
 
 ```bash
 # Option 1: Extract from SUMMARY frontmatter
-SUMMARY_FILES=$(node ~/.claude/get-shit-done/bin/gsd-tools.cjs summary-extract "$PHASE_DIR"/*-SUMMARY.md --fields key-files)
+SUMMARY_FILES=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" summary-extract "$PHASE_DIR"/*-SUMMARY.md --fields key-files)
 
 # Option 2: Verify commits exist (if commit hashes documented)
 COMMIT_HASHES=$(grep -oE "[a-f0-9]{7,40}" "$PHASE_DIR"/*-SUMMARY.md | head -10)
 if [ -n "$COMMIT_HASHES" ]; then
-  COMMITS_VALID=$(node ~/.claude/get-shit-done/bin/gsd-tools.cjs verify commits $COMMIT_HASHES)
+  COMMITS_VALID=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" verify commits $COMMIT_HASHES)
 fi
 
 # Fallback: grep for files

bin/install.js

@@ -951,16 +951,16 @@ function cleanupOrphanedHooks(settings) {
     console.log(`  ${green}✓${reset} Removed orphaned hook registrations`);
   }
 
-  // Fix #330: Update statusLine if it points to old statusline.js path
+  // Fix #330: Update statusLine if it points to old GSD statusline.js path
+  // Only match the specific old GSD path pattern (hooks/statusline.js),
+  // not third-party statusline scripts that happen to contain 'statusline.js'
   if (settings.statusLine && settings.statusLine.command &&
-      settings.statusLine.command.includes('statusline.js') &&
-      !settings.statusLine.command.includes('gsd-statusline.js')) {
-    // Replace old path with new path
+      /hooks[\/\\]statusline\.js/.test(settings.statusLine.command)) {
     settings.statusLine.command = settings.statusLine.command.replace(
-      /statusline\.js/,
-      'gsd-statusline.js'
+      /hooks([\/\\])statusline\.js/,
+      'hooks$1gsd-statusline.js'
     );
-    console.log(`  ${green}✓${reset} Updated statusline path (statusline.js → gsd-statusline.js)`);
+    console.log(`  ${green}✓${reset} Updated statusline path (hooks/statusline.js → hooks/gsd-statusline.js)`);
   }
 
   return settings;

commands/gsd/debug.md

@@ -31,12 +31,12 @@ ls .planning/debug/*.md 2>/dev/null | grep -v resolved | head -5
 ## 0. Initialize Context
 
 ```bash
-INIT=$(node ~/.claude/get-shit-done/bin/gsd-tools.cjs state load)
+INIT=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" state load)
 ```
 
 Extract `commit_docs` from init JSON. Resolve debugger model:
 ```bash
-DEBUGGER_MODEL=$(node ~/.claude/get-shit-done/bin/gsd-tools.cjs resolve-model gsd-debugger --raw)
+debugger_model=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" resolve-model gsd-debugger --raw)
 ```
 
 ## 1. Check Active Sessions

commands/gsd/research-phase.md

@@ -34,20 +34,20 @@ Normalize phase input in step 1 before any directory lookups.
 ## 0. Initialize Context
 
 ```bash
-INIT=$(node ~/.claude/get-shit-done/bin/gsd-tools.cjs init phase-op "$ARGUMENTS")
+INIT=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" init phase-op "$ARGUMENTS")
 ```
 
 Extract from init JSON: `phase_dir`, `phase_number`, `phase_name`, `phase_found`, `commit_docs`, `has_research`, `state_path`, `requirements_path`, `context_path`, `research_path`.
 
 Resolve researcher model:
 ```bash
-RESEARCHER_MODEL=$(node ~/.claude/get-shit-done/bin/gsd-tools.cjs resolve-model gsd-phase-researcher --raw)
+RESEARCHER_MODEL=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" resolve-model gsd-phase-researcher --raw)
 ```
 
 ## 1. Validate Phase
 
 ```bash
-PHASE_INFO=$(node ~/.claude/get-shit-done/bin/gsd-tools.cjs roadmap get-phase "${phase_number}")
+PHASE_INFO=$(node "$HOME/.claude/get-shit-done/bin/gsd-tools.cjs" roadmap get-phase "${phase_number}")
 ```
 
 **If `found` is false:** Error and exit. **If `found` is true:** Extract `phase_number`, `phase_name`, `goal` from JSON.