- <!-- JAL-4298 --> Java Console opening at startup with the exampleFile_v2_7.jvp opening (nearly always) causes Jalview to hang
- <!-- JAL-4282 --> automatic positioning of ID width for imported project can fail for certain font size configured in User preferences (affects most versions of Jalview prior to 2.11.3.0)
- <!-- JAL-4223 --> RNAML import missing terminal residue
+- <!-- JAL-4218 --> Jalview source distribution unnecessarily includes dist directory with built jalview jar and dependencies
## New Known defects
- <!-- JAL-4303 --> EBI-AlphaFold PLDDT colours cannot be overlaid on alignment via 'Colour by annotation' unless the alignment's colourscheme has been set to 'None' via the Colours menu.
- <!-- 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
- <!-- JAL-4323 --> scripts adding new fileformats or colourschemes do not work when run via command line
+- <!-- JAL-4290 --> Headless alignment export with structure annotations doesn't include secondary structure and temperature factor