+- <!-- JAL-2353 --> Show Crossrefs fails to retrieve CDS from ENA or Ensembl for sequences retrieved from Uniprot due to version numbers in cross-reference accession
+- <!-- JAL-4334 --> Uniprot parser fails to import sequences with features that have 'unknown' start or end
+- <!-- JAL-4184 --> Stockholm export does not include sequence descriptions
+- <!-- JAL-4075 --> Don't add string label version of DSSP secondary structure codes in secondary structure annotation rows
+- <!-- JAL-4182 --> reference annotation not correctly transferred to alignment containing a sub-sequence when a selection is active
+- <!-- JAL-4177 --> Can press 'Add' or 'New View' multiple times when manually adding and viewing a 3D structure via structure chooser
+- <!-- JAL-4311 --> 3D beacons sources providing models scored with PLDDT and pTM not sorted against alphaFoldDB models
+- <!-- JAL-4133 --> Jalview project does not preserve font aspect ratio when Viewport is zoomed with mouse
+- <!-- JAL-4253,JAL-4293 --> Lower line of the sequence group border does not align with vertical and background residue box
+- <!-- JAL-4128 --> Resizing overview quickly with solid-drags enabled causes exception
+- <!-- JAL-4150 --> Sequences copied to clipboard from within Jalview cannot be pasted via the desktop's popup menu to a new alignment window
+- <!-- JAL-2528, JAL-1713 --> Overview window is saved in project file, and state of 'show hidden regions' is preserved.
+- <!-- JAL-4153 --> JvCacheableInputBoxTest flaky on build server
+- <!-- JAL-4255 --> SLF4J produces an error to STDERR at Jalview startup due to missing class
+- <!-- JAL-4189 --> macOS Dock and KDE taskbar names Jalview icon "java" when running jalview via the getdown app launcher
+- <!-- JAL-2910 --> HeadlessException in console in headless mode (actually fixed in 2.11.{0,1,2))
+- <!-- JAL-3783 --> Groovy console does not open when Jalview launched from jalview's Java 11 executable jar (available via conda) for recent versions of groovy
+- <!-- JAL-4310 --> Don't offer View model page for sources that do not have model pages
+- <!-- 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-3088 --> RNA secondary structure annotation final-ending-solo-brace arrow points the wrong way
+- <!-- JAL-4218 --> Jalview source distribution unnecessarily includes dist directory with built jalview jar and dependencies
+- <!-- JAL-3921 --> Jmol sessions involving large molecules may not be fully saved in Jalview project files (known defect in 2.11.2.x)
+
+
+### New Known Issues
+- <!-- 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-4302 --> Tree renderer doesn't show bottom-most leaves of tree when Fit-To-Window is enabled.
+- <!-- JAL-4338 --> PAE partition not shown in the same place when tree is closed and reopened
+- <!-- JAL-4178 --> Cannot cancel structure view open action once it has been started via the structure chooser dialog
+- <!-- JAL-4142 --> Example project's multiple views do not open in distinct locations when eXpand views is used to show them all separately
+- <!-- JAL-4127 --> 'Reload' for a jalview project results in all windows being duplicated (since 2.11.2.6, more severe in 2.11.3.0)
+- <!-- JAL-4325 --> Overview shown and then closed when importing legacy jalview projects without overview store/restore information
+- <!-- 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
+- <!-- 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
+- <!-- JAL-4151 --> Copy sequences from one alignment and Pasting as new window in another alignment doesn't propagate title from original alignment's window
+- <!-- JAL-4157 --> Annotation colouring dialog box doesn't remember 'use original colours' settings when opened via the Colour menu
+- <!-- JAL-4327 --> When the Groovy console is open Jalview does not prompt to save before quitting
+- <!-- JAL-4328 --> Jalview works with but is not fully compatible with latest Ensembl REST API (15.6)
+