refactor: fix logic issues and code optimization

- Fix remoteInput variable sharing bug in displaySetupSection
- Fix renamed/copied file path handling to use new path
- Fix setHasConflicts command duplication issue
- Fix conflict status detection order in getFileStatuses
- Remove redundant optional parameter from calculateFolderStatuses
- Remove unused pull import from settings.ts
- Refactor status badge refresh with proper timeout cleanup
- Add void to command callbacks

Author: whtiehack