MEGA12 (CLI): versionet e vjetra dhe historiku

Bug Fixes
- Fixes an error when cancelling ML tree construction with bootstrap where Tree Explorer would display the topology from the last completed replicate.

Bug Fixes
- Name and divergence time searches using the Timetree resource have been updated to use the new Timetree API URLs.
- Distance calculations using the Pamilo-Bianchi-Li and Li-Wu-Luo methods for dN and dS estimation on Windows operating systems have been fixed.
- Scale bar positioning for trees displayed in the radial style has been updated to avoid overlapping with taxa names.
- Missing citation for MEGA 12.1 on Linux operating systems has been fixed.

Updates
- The installers for Windows operating systems are now code-signed.
Bug Fixes
- Ancestral sequence inference when using the UCSC 46-species tree has been updated to maintain the correct tree rooting. This is part of the mutation diagnosis analysis.
- Fixed size and positioning of components when using the Calibration Editor on high dpi monitors.
- Refactored naive mapping of taxa groups that was sluggish for very large data.
- Fixed an access violation when using the prototyper to generate a .mao file for Reltime with branch lengths.

Bug Fixes
- Fixes an access violation in the Calibration Editor when overwriting an existing calibration.
- Fixes a memory leak in Maximum Likelihood tree construction with bootstrap.
- On Linux, fixes an incorrect count of the number of processors available.
- For the position-by-position rates analysis, use the number of threads specified by the user.
- Fixes an error in the Sequence Data Explorer where the genes/domains popup menu was displayed along with groups popup menu.
- Fixes incorrect row mapping for the groups context menu in the Sequence Data Explorer.
- Fixes false detection of user cancellation for very small data when doing Maximum Likelihood tree construction.

Bug Fixes
- Fixes the path to the MUSCLE executable for the 32-bit version of MEGA12.
- When exporting trees to Newick files, always use the period character regardless of locale.
- Updates the URL for DrPhylo help to use the correct github branch.
- Fixes a "list index out of bounds" error when sorting groupwise distance matrix results.
- Synchronizes threads for the Mutation Diagnosis tool.