fix(beads): prevent routes.jsonl corruption and add doctor check for rig-level routes.jsonl (#377)

* fix(beads): prevent routes.jsonl corruption from bd auto-export

When issues.jsonl doesn't exist, bd's auto-export mechanism writes
issue data to routes.jsonl, corrupting the routing configuration.

Changes:
- install.go: Create issues.jsonl before routes.jsonl at town level
- manager.go: Create issues.jsonl in rig beads; don't create routes.jsonl
  (rig-level routes.jsonl breaks bd's walk-up routing to town routes)
- Add integration tests for routes.jsonl corruption prevention

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

* fix(doctor): add check to detect and fix rig-level routes.jsonl

Add RigRoutesJSONLCheck to detect routes.jsonl files in rig .beads
directories. These files break bd's walk-up routing to town-level
routes.jsonl, causing cross-rig routing failures.

The fix unconditionally deletes rig-level routes.jsonl files since
bd will auto-export to issues.jsonl on next run.

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

* test(rig): add verification that routes.jsonl does NOT exist in rig .beads

Add explicit test assertion and detailed comment explaining why rig-level
routes.jsonl files must not exist (breaks bd walk-up routing to town routes).

Also verify that issues.jsonl DOES exist (prevents bd auto-export corruption).

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

* fix(doctor): ensure town root route exists in routes.jsonl

The RoutesCheck now detects and fixes missing town root routes (hq- -> .).
This can happen when routes.jsonl is corrupted or was created without the
town route during initialization.

Changes:
- Detect missing hq- route in Run()
- Add hq- route in Fix() when missing
- Handle case where routes.jsonl is corrupted (regenerate with town route)
- Add comprehensive unit tests for route detection and fixing

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

* test(beads): fix routing integration test for routes.jsonl corruption

The TestBeadsRoutingFromTownRoot test was failing because bd's auto-export
mechanism writes issue data to routes.jsonl when issues.jsonl doesn't exist.
This corrupts the routing configuration.

Fix: Create empty issues.jsonl after bd init to prevent corruption.
This mirrors what gt install does to prevent the same bug.

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

---------

Co-authored-by: julianknutsen <julianknutsen@users.noreply.github>
Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>

internal/rig/manager.go

@@ -635,19 +635,21 @@ func (m *Manager) initBeads(rigPath, prefix string) error {
 	// Ignore errors - fingerprint is optional for functionality
 	_, _ = migrateCmd.CombinedOutput()
 
-	// Add route from rig beads to town beads for cross-database resolution.
-	// This allows rig beads to resolve hq-* prefixed beads (role beads, etc.)
-	// that are stored in town beads.
-	townRoute := beads.Route{Prefix: "hq-", Path: ".."}
-	if err := beads.AppendRouteToDir(beadsDir, townRoute); err != nil {
-		// Non-fatal: role slot set will fail but agent beads still work
-		fmt.Printf("   ⚠ Could not add route to town beads: %v\n", err)
+	// Ensure issues.jsonl exists to prevent bd auto-export from corrupting other files.
+	// bd init creates beads.db but not issues.jsonl in SQLite mode.
+	// Without issues.jsonl, bd's auto-export might write issues to other .jsonl files.
+	issuesJSONL := filepath.Join(beadsDir, "issues.jsonl")
+	if _, err := os.Stat(issuesJSONL); os.IsNotExist(err) {
+		if err := os.WriteFile(issuesJSONL, []byte{}, 0644); err != nil {
+			// Non-fatal but log it
+			fmt.Printf("   ⚠ Could not create issues.jsonl: %v\n", err)
+		}
 	}
 
-	typesCmd := exec.Command("bd", "config", "set", "types.custom", constants.BeadsCustomTypes)
-	typesCmd.Dir = rigPath
-	typesCmd.Env = filteredEnv
-	_, _ = typesCmd.CombinedOutput()
+	// NOTE: We intentionally do NOT create routes.jsonl in rig beads.
+	// bd's routing walks up to find town root (via mayor/town.json) and uses
+	// town-level routes.jsonl for prefix-based routing. Rig-level routes.jsonl
+	// would prevent this walk-up and break cross-rig routing.
 
 	return nil
 }