Improve bd doctor JSONL checks to focus on real problems

Previously bd doctor warned about using beads.jsonl vs issues.jsonl, but
users should be free to configure any name they want. The real problems are:
1. Having multiple JSONL files (sync/merge conflicts)
2. Configuration not matching reality

Changes:
- Rewrote CheckLegacyJSONLFilename to scan for ALL .jsonl files
- Now filters out merge artifacts (backup, .orig, .bak, etc.)
- Warns only when multiple real JSONL files exist
- Added CheckDatabaseConfig to detect when configured paths do not match
  what actually exists on disk
- Updated tests to verify backup files are ignored
- Added test cases for custom JSONL filenames

🤖 Generated with Claude Code
Co-Authored-By: Claude <noreply@anthropic.com>

cmd/bd/doctor/legacy_test.go

@@ -190,20 +190,38 @@ func TestCheckLegacyJSONLFilename(t *testing.T) {
 			expectWarning:  false,
 		},
 		{
-			name:           "canonical issues.jsonl",
+			name:           "single issues.jsonl",
 			files:          []string{"issues.jsonl"},
 			expectedStatus: "ok",
 			expectWarning:  false,
 		},
 		{
-			name:           "non-standard beads.jsonl",
+			name:           "single beads.jsonl is ok",
 			files:          []string{"beads.jsonl"},
+			expectedStatus: "ok",
+			expectWarning:  false,
+		},
+		{
+			name:           "custom name is ok",
+			files:          []string{"my-issues.jsonl"},
+			expectedStatus: "ok",
+			expectWarning:  false,
+		},
+		{
+			name:           "multiple JSONL files warning",
+			files:          []string{"beads.jsonl", "issues.jsonl"},
 			expectedStatus: "warning",
 			expectWarning:  true,
 		},
 		{
-			name:           "both files present",
-			files:          []string{"beads.jsonl", "issues.jsonl"},
+			name:           "backup files ignored",
+			files:          []string{"issues.jsonl", "issues.jsonl.backup", "BACKUP_issues.jsonl"},
+			expectedStatus: "ok",
+			expectWarning:  false,
+		},
+		{
+			name:           "multiple real files with backups",
+			files:          []string{"issues.jsonl", "beads.jsonl", "issues.jsonl.backup"},
 			expectedStatus: "warning",
 			expectWarning:  true,
 		},