fix: doctor deletions check and onboard docs improvements

- Fix doctor to treat empty deletions.jsonl as valid (0 entries OK status)
- Fix HydrateDeletionsManifest to create empty file when no deletions found
- Add --parent flag documentation to onboard command
- Add CLI --help tip throughout onboard documentation

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

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

cmd/bd/onboard.go

@@ -63,6 +63,7 @@ bd stale --days 30 --json          # Forgotten issues
 
 # Create and manage
 bd create "Title" -t bug|feature|task -p 0-4 --json
+bd create "Subtask" --parent <epic-id> --json  # Hierarchical subtask
 bd update <id> --status in_progress --json
 bd close <id> --reason "Done" --json
 
@@ -128,12 +129,18 @@ Use the beads MCP server for native function calls instead of shell commands:
 - **README.md** - User-facing documentation
 - **docs/CLI_REFERENCE.md** - Complete command reference
 
+## CLI Help
+
+Run ` + "`bd <command> --help`" + ` to see all available flags for any command.
+For example: ` + "`bd create --help`" + ` shows ` + "`--parent`" + `, ` + "`--deps`" + `, ` + "`--assignee`" + `, etc.
+
 ## Important Rules
 
 - ✅ Use bd for ALL task tracking
 - ✅ Always use ` + "`--json`" + ` flag for programmatic use
 - ✅ Run ` + "`bd sync`" + ` at end of sessions
 - ✅ Test with ` + "`BEADS_DB=/tmp/test.db`" + `
+- ✅ Run ` + "`bd <cmd> --help`" + ` to discover available flags
 - ❌ Do NOT create markdown TODO lists
 - ❌ Do NOT create test issues in production DB
 - ❌ Do NOT commit ` + "`.beads/beads.db`" + ` (JSONL only)
@@ -164,6 +171,7 @@ bd ready --json
 ` + "```bash" + `
 bd create "Issue title" -t bug|feature|task -p 0-4 --json
 bd create "Issue title" -p 1 --deps discovered-from:bd-123 --json
+bd create "Subtask" --parent <epic-id> --json  # Hierarchical subtask (gets ID like epic-id.1)
 ` + "```" + `
 
 **Claim and update:**
@@ -263,6 +271,11 @@ history/
 - ✅ Preserves planning history for archeological research
 - ✅ Reduces noise when browsing the project
 
+### CLI Help
+
+Run ` + "`bd <command> --help`" + ` to see all available flags for any command.
+For example: ` + "`bd create --help`" + ` shows ` + "`--parent`" + `, ` + "`--deps`" + `, ` + "`--assignee`" + `, etc.
+
 ### Important Rules
 
 - ✅ Use bd for ALL task tracking
@@ -270,6 +283,7 @@ history/
 - ✅ Link discovered work with ` + "`discovered-from`" + ` dependencies
 - ✅ Check ` + "`bd ready`" + ` before asking "what should I work on?"
 - ✅ Store AI planning docs in ` + "`history/`" + ` directory
+- ✅ Run ` + "`bd <cmd> --help`" + ` to discover available flags
 - ❌ Do NOT create markdown TODO lists
 - ❌ Do NOT use external issue trackers
 - ❌ Do NOT duplicate tracking systems