fix: Windows shell robustness, project_root detection, and hook stdin safety (#1343)

Address 4 root causes of Windows + Claude Code reliability issues:

1. Workflow shell robustness: add || true guards to informational commands
   (ls, grep, find, cat) that return non-zero on "no results", preventing
   workflow step failures under strict execution models. Guard glob loops
   with [ -e "$var" ] || continue to handle empty glob expansion.

2. Hook stdin handling: replace readFileSync('/dev/stdin') with async
   process.stdin + timeout in agent templates (gsd-verifier.md). Existing
   JS hooks already have timeout guards.

3. project_root detection: fix isInsideGitRepo() to check .git at the
   candidate parent level (not just below it), enabling correct detection
   when .git and .planning/ are siblings at the same directory level —
   the common single-repo case from a subdirectory.

4. @file: handoff: add missing @file: handlers to autonomous.md and
   manager.md workflows that call gsd-tools init but lacked the handler
   for large output payloads.

Fixes #1343

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

get-shit-done/workflows/pause-work.md

@@ -13,7 +13,7 @@ Find current phase directory from most recently modified files:
 
 ```bash
 # Find most recent phase directory with work
-ls -lt .planning/phases/*/PLAN.md 2>/dev/null | head -1 | grep -oP 'phases/\K[^/]+'
+(ls -lt .planning/phases/*/PLAN.md 2>/dev/null || true) | head -1 | grep -oP 'phases/\K[^/]+' || true
 ```
 
 If no active phase detected, ask user which phase they're pausing work on.
@@ -36,7 +36,7 @@ Ask user for clarifications if needed via conversational questions.
 **Also inspect SUMMARY.md files for false completions:**
 ```bash
 # Check for placeholder content in existing summaries
-grep -l "To be filled\|placeholder\|TBD" .planning/phases/*/*.md 2>/dev/null
+grep -l "To be filled\|placeholder\|TBD" .planning/phases/*/*.md 2>/dev/null || true
 ```
 Report any summaries with placeholder content as incomplete items.
 </step>