+- <!-- JAL-4064 --> Native M1 build for macOS using Adoptium JRE 11 macos-aarch64
+- <!-- JAL-3416 --> Jalview now uses a standard 'look and feel' (FlatLaf) on Linux, OSX and everywhere else
+- <!-- JAL-4019 --> Ambiguous Base Colourscheme
+- <!-- JAL-4061 --> Find can search sequence features' type and description
+- <!-- JAL-4062 --> Hold down Shift + CMD/CTRL C to copy highlighted regions as new sequences
+- <!-- JAL-1556 --> Quickly enable select and/or colour by for displayed annotation row via annotation panel popup menu
+- <!-- JAL-4094 --> Shift+Click+Drag to adjust height of all annotation tracks of same type
+- <!-- JAL-4190 --> Pressing escape in tree panel clears any current selection
+- <!-- JAL-4089 --> Use selected columns for superposition
+- <!-- JAL-4086 --> Highlight aligned positions on all associated structures when mousing over a column
+- <!-- JAL-4221 --> sequence descriptions are updated from database reference sources if not already defined
+- <!-- JAL-4273 --> Visible adjuster marks to grab and adjust annotation panel height and id width
+- <!-- JAL-4260 --> Adjustable ID margin when alignment is wrapped
+- <!-- JAL-4274 --> Command line options and configurable bitmap export (via preferences file) for height, width and scale factor
+- <!-- JAL-4307 --> Show or hide ligands in a Jmol structure view via View Ligands submenu
+- <!-- JAL-4252 --> Jmol's display is antialiased by default (smoother, less pixellated)
+
+### Improved support for working with structures and computationally determined models
+- <!-- JAL-3895 --> Alphafold red/orange/yellow/green colourscheme for structures
+- <!-- JAL-4095 --> Interactive picking of low pAE score regions
+- <!-- JAL-4027, JAL-3858, JAL-2292 --> Predicted Alignment Error annotation tracks for structures from AlphaFold DB
+- <!-- JAL-4033 --> Selections with visual feedback via contact matrix annotation
+- <!-- JAL-3855 --> Discover and import alphafold2 models and metadata from https://alphafold.ebi.ac.uk/
+- <!-- JAL-4091 --> Visual indication of relationship with associated sequence to distinguish different sequence associated annotation rows
+- <!-- JAL-4123 --> GUI and command line allows configuration of how temperature factor in imported 3D structure data should be interpreted
+- <!-- JAL-3914 --> Import model reliability scores encoded as temperature factor annotation with their correct name and semantics
+- <!-- JAL-3858 --> Import and display alphafold alignment uncertainty matrices from JSON
+- <!-- JAL-4134,JAL-4158 --> Column-wise alignment groups and selections and interactive tree viewer for PAE matrices
+- <!-- JAL-4124 --> Store/Restore PAE data and visualisation settings from Jalview Project
+- <!-- JAL-4281 --> Store and restore adjustable ID margin and annotation panel height in Jalview projects
+- <!-- JAL-4083 --> Multiple residue sidechain highlighting in structure viewers from PAE mouseovers
+- <!-- JAL-4147 --> Per-structure and chain shown when annotation shown sorted by label enabling secondary structure and temperature factor scores from different chains and structures for the same sequence to be visually compared.
+
+
+### Jalview on the command line
+- <!-- 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-3830 --> Command-line wrapper script for macOS bundle, linux and Windows installations (bash, powershell and .bat wrappers)
+- <!-- 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-4195,JAL-4194,JAL-4193 --> sensible responses from the CLI when things go wrong during image export
+- Add a command line option to set Jalview properties for this session only
+- Add a command line option to suppress opening the startup file for this session
+
+### Other improvements
+- <!-- JAL-4250 --> Secondary structure annotation glyphs are rendered anti-aliasing when enabled
+- <!-- JAL-325 --> Helix and Sheet glyphs vertically centered with respect to grey coil secondary structure annotation track
+- <!-- JAL-4317 --> feature should be displayed when its rendering and filtering settings are adjusted
+- <!-- JAL-4250 --> Updated JFreeSVG (https://www.jfree.org/jfreesvg) from 2.1 to 3.4.3
+- <!-- JAL-3119 --> Name of alignment and view included in overview window's title
+- <!-- JAL-4213 --> "add reference annotation" add all positions in reference annotation tracks, not just positions in the currently highlighted columns/selection range
+- <!-- JAL-4119 --> EMBL-EBI SIFTS file downloads now use split directories
+- <!-- JAL-3820 --> In Linux desktops' task-managers, the grouped Jalview windows get a generic name
+- <!-- 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
+- <!-- JAL-4308 --> Reduce number of database crossreferences shown in tooltip
+- <!-- JAL-4315 --> Drag and drop feature colours file on an alignment to quickly apply feature settings
+- <!-- JAL-3676 --> Allow log level configuration via Jalview's Java Console, and a Copy to Clipboard button
+- <!-- JAL-4304,JAL-4305 --> Upgrade bundled groovy to v4.0.15 and regularised interface for groovy scripts run from CLI, interactively and headlessly.
+
+### Development and Deployment
+- <!-- JAL-4054 --> Installers built with install4j10
+- <!-- JAL-4167 --> Create separate gradle test task for some tests
+- <!-- JAL-4212 --> Prevent gradle test on macOS continuously grabbing focus
+- <!-- JAL-4111 --> Allow gradle build to create suffixed DEVELOP-... builds with channel appbase
+- <!-- JAL-4288 --> Update .jvl generation in build.gradle for jalview branch builds
+- <!-- JAL-4243 --> Jalview bio.tools description maintained under jalview's git repo and bundled with source release
+- <!-- JAL-4110 --> Output stderr and stdout when running tests via gradle
+- <!-- JAL-3599 --> New gradle task providing runtime acceptance test for JalviewJS based on Chromium for Tests (still work in progress)