refactor: Simplify wisp architecture - badges not separate storage

Wisps are now just issues with Wisp=true flag in the main database,
not exported to JSONL. Removes all references to .beads-wisp/ directory.

- Update docs: CLAUDE.md, CLI_REFERENCE.md, MOLECULES.md, DELETIONS.md
- Update code comments: wisp.go
- Update changelog and info.go version notes

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

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

CHANGELOG.md

@@ -275,13 +275,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - `bd wisp create <proto>` - Instantiate proto as ephemeral wisp (solid→vapor)
   - `bd wisp list` - List all wisps with stale detection
   - `bd wisp gc` - Garbage collect orphaned wisps
-  - Wisps live in `.beads-wisp/` (gitignored), never sync to remote
+  - Wisps have Wisp=true flag and are not exported to JSONL (never sync)
 
 - **Chemistry UX commands** - Phase-aware molecule operations
   - `bd pour <proto>` - Instantiate proto as persistent mol (solid→liquid)
   - `bd mol bond --wisp` - Force spawn as vapor when attaching to mol
   - `bd mol bond --pour` - Force spawn as liquid when attaching to wisp
-  - Cross-store squash: condense wisp to digest in main storage
+  - Squash clears Wisp flag, promoting to persistent (exported to JSONL)
 
 - **Cross-project dependencies** (bd-66w1, bd-om4a) - Reference issues across repos
   - `external:<repo>:<id>` dependency syntax
@@ -302,7 +302,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
-- **Wisp storage initialization** - NewWispStorage now copies issue_prefix from main db
+- **Wisp flag handling** - Wisps now use Wisp=true flag in main database (not exported to JSONL)
 - **Prefix validation in multi-repo mode** (GH#686) - Skip validation for external repos
 - **Empty config values** (GH#680, GH#684) - Handle gracefully in getRepoConfig()
 - **Doctor UX improvements** (GH#687) - Better diagnostics and daemon integration

CLAUDE.md

@@ -317,7 +317,7 @@ bd uses a molecular chemistry metaphor for template instantiation:
 |-------|---------|--------|----------|
 | **Proto** (solid) | Built-in | N/A | Reusable templates |
 | **Mol** (liquid) | `.beads/` | Yes | Persistent work |
-| **Wisp** (vapor) | `.beads-wisp/` | No | Ephemeral operations |
+| **Wisp** (vapor) | `.beads/` (Wisp=true) | No | Ephemeral operations |
 
 **Instantiation commands:**
 
@@ -326,7 +326,7 @@ bd uses a molecular chemistry metaphor for template instantiation:
 bd pour <proto> --var key=value      # Create in .beads/
 
 # Wisp: proto → ephemeral wisp (vapor phase)
-bd wisp create <proto> --var key=value  # Create in .beads-wisp/
+bd wisp create <proto> --var key=value  # Wisp=true, not exported to JSONL
 
 # List available templates
 bd mol list --json

cmd/bd/info.go

@@ -341,7 +341,7 @@ var versionChanges = []VersionChange{
 			"NEW: Chemistry UX - bd pour, bd mol bond --wisp/--pour for phase control",
 			"NEW: Cross-project deps - external:<repo>:<id> syntax, bd ship command",
 			"BREAKING: bd repo add/remove now writes to .beads/config.yaml (not DB)",
-			"FIX: Wisp storage auto-copies issue_prefix from main database",
+			"FIX: Wisps use Wisp=true flag in main database (not exported to JSONL)",
 		},
 	},
 	{

cmd/bd/wisp.go

@@ -75,9 +75,9 @@ var wispCreateCmd = &cobra.Command{
 	Long: `Create a wisp from a proto - sublimation from solid to vapor.
 
 This is the chemistry-inspired command for creating ephemeral work from templates.
-The resulting wisp lives in .beads-wisp/ (ephemeral storage) and is NOT synced.
+The resulting wisp is stored in the main database with Wisp=true and NOT exported to JSONL.
 
-Phase transition: Proto (solid) -> wisp -> Wisp (vapor)
+Phase transition: Proto (solid) -> Wisp (vapor)
 
 Use wisp create for:
   - Patrol cycles (deacon, witness)
@@ -86,8 +86,8 @@ Use wisp create for:
   - Routine operations with no audit value
 
 The wisp will:
-  - Be stored in .beads-wisp/ (gitignored)
-  - NOT sync to remote
+  - Be stored in main database with Wisp=true flag
+  - NOT be exported to JSONL (and thus not synced via git)
   - Either evaporate (burn) or condense to digest (squash)
 
 Examples:

docs/CLI_REFERENCE.md

@@ -351,7 +351,7 @@ Beads uses a chemistry metaphor for template-based workflows. See [MOLECULES.md]
 |-------|-------|---------|---------|
 | Solid | Proto | `.beads/` | `bd mol catalog` |
 | Liquid | Mol | `.beads/` | `bd pour` |
-| Vapor | Wisp | `.beads-wisp/` | `bd wisp create` |
+| Vapor | Wisp | `.beads/` (Wisp=true, not exported) | `bd wisp create` |
 
 ### Proto/Template Commands
 

docs/DELETIONS.md

@@ -230,11 +230,10 @@ This is intentional, not a bug. See [ARCHITECTURE.md](ARCHITECTURE.md#wisps-and-
 
 ### If You Need Wisp History
 
-Wisps exist in local git history (SQLite database commits) until garbage collected. Future enhancements may include:
+Wisps are stored in the main database with `Wisp=true` flag and are not exported to JSONL. They exist in local SQLite until garbage collected or squashed. Future enhancements may include:
 
-- Separate ephemeral repository for wisp storage
-- Explicit migration step to promote wisps to permanent storage
 - Configurable wisp retention policies
+- Automatic staleness detection based on dependency graph pressure
 
 ## Related
 

docs/MOLECULES.md

@@ -123,7 +123,7 @@ For reusable workflows, beads uses a chemistry metaphor:
 |-------|------|---------|--------|---------|
 | **Solid** | Proto | `.beads/` | Yes | Frozen template |
 | **Liquid** | Mol | `.beads/` | Yes | Active persistent work |
-| **Vapor** | Wisp | `.beads-wisp/` | No | Ephemeral operations |
+| **Vapor** | Wisp | `.beads/` (Wisp=true) | No | Ephemeral operations |
 
 ### Phase Commands