refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

Analysis found these commands are dead code:
- gt never calls `bd pin` - uses `bd update --status=pinned` instead
- Beads.Pin() wrapper exists but is never called
- bd hook functionality duplicated by gt mol status
- Code comment says "pinned field is cosmetic for bd hook visibility"

Removed:
- cmd/bd/pin.go
- cmd/bd/unpin.go
- cmd/bd/hook.go

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

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

docs/MOLECULES.md

@@ -128,8 +128,8 @@ For reusable workflows, beads uses a chemistry metaphor:
 ### Phase Commands
 
 ```bash
-bd pour <proto>                  # Proto → Mol (persistent instance)
-bd wisp create <proto>           # Proto → Wisp (ephemeral instance)
+bd mol pour <proto>              # Proto → Mol (persistent instance)
+bd mol wisp <proto>              # Proto → Wisp (ephemeral instance)
 bd mol squash <id>               # Mol/Wisp → Digest (permanent record)
 bd mol burn <id>                 # Wisp → nothing (discard)
 ```
@@ -227,10 +227,10 @@ bd close <id> --reason "Done"
 Wisps accumulate if not squashed/burned:
 
 ```bash
-bd wisp list           # Check for orphans
-bd mol squash <id>     # Create digest
-bd mol burn <id>       # Or discard
-bd wisp gc             # Garbage collect old wisps
+bd mol wisp list        # Check for orphans
+bd mol squash <id>      # Create digest
+bd mol burn <id>        # Or discard
+bd mol wisp gc          # Garbage collect old wisps
 ```
 
 ## Layer Cake Architecture
@@ -238,49 +238,18 @@ bd wisp gc             # Garbage collect old wisps
 For reference, here's how the layers stack:
 
 ```
-Formulas (.formula.json)                  ← SOURCE: shareable workflow definitions
-    ↓ cook (ephemeral)
-[Protos]                                  ← TRANSIENT: compiled templates (auto-deleted)
-    ↓ pour/wisp
-Molecules (bond, squash, burn)            ← EXECUTION: workflow operations
+Formulas (JSON compile-time macros)      ← optional, for complex composition
+    ↓
+Protos (template issues)                  ← optional, for reusable patterns
+    ↓
+Molecules (bond, squash, burn)            ← workflow operations
     ↓
 Epics (parent-child, dependencies)        ← DATA PLANE (the core)
     ↓
 Issues (JSONL, git-backed)                ← STORAGE
 ```
 
-**Protos are ephemeral**: When you `bd pour formula-name` or `bd wisp create formula-name`, the formula is cooked into a temporary proto, used to spawn the mol/wisp, then automatically deleted. Protos are an implementation detail, not something users manage directly.
-
-**Most users only need the bottom two layers.** Formulas are for sharing reusable patterns.
-
-## Distillation: Extracting Patterns
-
-The lifecycle is circular - you can extract formulas from completed work:
-
-```
-Formulas ──cook──→ Mols/Wisps ──distill──→ Formulas
-```
-
-**Use cases for distillation:**
-- **Emergent patterns**: Manually structured an epic that worked well
-- **Modified execution**: Poured a formula but added custom steps
-- **Learning from success**: Extract what made a complex mol succeed
-
-```bash
-bd distill <mol-id> -o my-workflow.formula.json   # Extract formula from mol
-```
-
-## Sharing: The Mol Mall
-
-All workflow sharing happens via formulas:
-
-```bash
-bd mol publish my-workflow.formula.json            # Share to GitHub repo
-bd mol install github.com/org/mol-code-review      # Install from GitHub
-bd pour mol-code-review --var repo=myproject       # Use installed formula
-```
-
-Formulas are clean source code: composable, versioned, parameterized. Mols contain execution-specific context and aren't shared directly.
+**Most users only need the bottom two layers.** Protos and formulas are for reusable patterns and complex composition.
 
 ## Commands Quick Reference
 
@@ -303,8 +272,8 @@ bd dep tree <id>                 # Show dependency tree
 ### Molecules
 
 ```bash
-bd pour <proto> --var k=v        # Template → persistent mol
-bd wisp create <proto>           # Template → ephemeral wisp
+bd mol pour <proto> --var k=v    # Template → persistent mol
+bd mol wisp <proto>              # Template → ephemeral wisp
 bd mol bond A B                  # Connect work graphs
 bd mol squash <id>               # Compress to digest
 bd mol burn <id>                 # Discard without record