### Jalview on the command line
-- <!-- JAL-4160,JAL-629 --> New command line argument framework allowing flexible batch processing, figure generation, and import of structures, pae matrices and other sequence associated data
+- <!-- JAL-4160,JAL-629,JAL-4262,JAL-4265, --> New command line argument framework allowing flexible batch processing, import of structures, pae matrices and other sequence associated data, and alignment and structure figure generation.
- <!-- JAL-4121 --> Assume --headless when jalview is run with a command line argument that generates output
- <!-- JAL-244 --> Automatically adjust Left margin on import to avoid cropping of annotation labels & sequence IDs
- <!-- JAL-901 --> Specify alignment title on import via --title argument
- <!-- JAL-4206 --> Improved file chooser's 'recent files' view and added filter for 'All known alignment files'
- <!-- JAL-4206 --> Relative files added to recent files list via import from command line are selected when Jalview opened from same location
+
## Still in progress (delete on release)
- <!-- JAL-4165 --> Missing last letter when copying consensus sequence from alignment if first column is hidden
- <!-- JAL-4261 --> Last sequence ID in alignment not shown and annotation labels are misaligned in HTML export
- <!-- JAL-3024 --> Files opened via command line with a relative path are added as relative paths to Recent files list (since 2.0.x)
+- <!-- JAL-4291 --> Test coverage for ID width adjustment disabled pending fix for new annotation label geometry and width calculation