Fix config system: rename config.json → metadata.json, fix config.yaml loading

- Renamed config.json to metadata.json to clarify purpose (database metadata)
- Fixed config.yaml/config.json conflict by making Viper explicitly load only config.yaml
- Added automatic migration from config.json to metadata.json on first read
- Fixed jsonOutput variable shadowing across 22 command files
- Updated bd init to create both metadata.json and config.yaml template
- Fixed 5 failing JSON output tests
- All tests passing

Resolves config file confusion and makes config.yaml work correctly.
Closes #178 (global flags), addresses config issues from #193

Amp-Thread-ID: https://ampcode.com/threads/T-e6ac8192-e18f-4ed7-83bc-4a5986718bb7
Co-authored-by: Amp <amp@ampcode.com>

cmd/bd/testdata/init.txt

@@ -2,7 +2,7 @@
 bd init --prefix test
 stdout 'initialized successfully'
 exists .beads/beads.db
-exists .beads/config.json
+exists .beads/metadata.json
 exists .beads/.gitignore
 grep '^\*\.db$' .beads/.gitignore
 grep '^\*\.db-journal$' .beads/.gitignore
@@ -12,4 +12,5 @@ grep '^daemon\.log$' .beads/.gitignore
 grep '^daemon\.pid$' .beads/.gitignore
 grep '^bd\.sock$' .beads/.gitignore
 grep '^!\*\.jsonl$' .beads/.gitignore
+grep '^!metadata\.json$' .beads/.gitignore
 grep '^!config\.json$' .beads/.gitignore