docs: Document deprecation timeline and add removal warnings (bd-pndo)

- Add Deprecated section to CHANGELOG.md listing all deprecated commands
- Set removal target: v1.0.0 for all deprecated commands
- Add '(will be removed in v1.0.0)' to all deprecation messages
- Add proper Deprecated field to admin_aliases.go (cleanup, compact, reset)
- Remove manual warning prints from admin aliases (Cobra handles it)

Deprecated commands documented:
- bd relate/unrelate → bd dep relate/unrelate
- bd daemons → bd daemon <subcommand>
- bd cleanup/compact/reset → bd admin <command>
- bd comment → bd comments add
- bd template* → bd mol/formula commands
- bd detect-pollution → bd doctor --check=pollution
- bd migrate-* → bd migrate <subcommand>

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

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

CHANGELOG.md

@@ -52,6 +52,30 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - Update jsonl_file_hash on import operations
   - Prevents spurious hash mismatch warnings
 
+### Deprecated
+
+The following commands are deprecated and will be removed in v1.0.0:
+
+- **`bd relate`** → use `bd dep relate` instead
+- **`bd unrelate`** → use `bd dep unrelate` instead
+- **`bd daemons`** → use `bd daemon <subcommand>` instead
+- **`bd cleanup`** → use `bd admin cleanup` instead
+- **`bd compact`** → use `bd admin compact` instead
+- **`bd reset`** → use `bd admin reset` instead
+- **`bd comment`** → use `bd comments add` instead
+- **`bd template`** → use `bd mol` instead
+- **`bd templates`** → use `bd formula list` instead
+- **`bd template show`** → use `bd mol show` instead
+- **`bd template bond`** → use `bd mol bond` instead
+- **`bd detect-pollution`** → use `bd doctor --check=pollution` instead
+- **`bd migrate-hash-ids`** → use `bd migrate hash-ids` instead
+- **`bd migrate-tombstones`** → use `bd migrate tombstones` instead
+- **`bd migrate-sync`** → use `bd migrate sync` instead
+- **`bd migrate-issues`** → use `bd migrate issues` instead
+
+All deprecated commands continue to work but print a warning. Update your scripts
+and muscle memory before v1.0.0 to avoid breakage.
+
 ### Changed
 
 - **Community tools documentation** (GH#772, GH#776)