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>

cmd/bd/comments.go

@@ -211,7 +211,7 @@ var commentCmd = &cobra.Command{
 	Args:       cobra.MinimumNArgs(1),
 	Run:        commentsAddCmd.Run,
 	Hidden:     true,
-	Deprecated: "use 'bd comments add' instead",
+	Deprecated: "use 'bd comments add' instead (will be removed in v1.0.0)",
 }
 
 func init() {