jalview

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Merge branch 'develop' into improvement/JAL-3830_macOS_bundle_wrapper

JAL-3248 Moved old README to doc/old_README and put pointers in new README for deskopt application building and JalviewJS building

JAL-3743 JAL-3745 Fixed NullPointerExceptions happening with linkCheck and jalviewjsTranspile tasks when gradle >= 6.6

JAL-3833 Allow setHiDPI and setHiDPIScale to work more usefully in real life

JAL-3833 cap the scaling used by HiDPISetting for incorrect DPI values or incorrect height/width values

JAL-3830 Improved jalview.bat to find either pwsh.exe or powershell.exe, and give better messages to the user

JAL-3830 BAT file wrapper around powershell, so jalview works in command prompt. Added install4j option for installer to add Jalview's bin dir to Path in Windows. Added install4j option to create symlink to bash script to user's local bin (first of ~/bin, ~/.local/bin, ~/local/bin, ~/opt/bin that exists. First two of these usually automatically in PATH).

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    /utils/getdown/bin/jalview.bat
JAL-3830 Follow all SymbolicLinks in Windows powershell wrapper

JAL-3830 delete channel.props and channel.propsv when uninstalling

JAL-3830 Moved wrappers to bin/jalview.* and make a symlink bin/jalview. Install4j script now jalviewg

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    /utils/getdown/bin/jalview.ps1
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    /utils/getdown/bin/jalview.sh
JAL-3830 Allow paths to start with '~'. Make path check more succinct.

JAL-3830 Now using a single universal bash script (jalviewc) for bash in linux, macos, cygwin and WSL. It keeps things together.

JAL-3830 add the windows bash script to getdown files and install4j installers

JAL-3830 bash script that works in both cygwin and WSL (Windows Subsystem for Linux)

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    /utils/getdown/jalviewc-windows
JAL-3830 Delete wrapper scripts and getdown *v files when uninstalling

JAL-3830 powershell wrapper tested on linux, macos and windows including spaces in paths. This is the way.

JAL-3830 minor fix in powershell wrapper

JAL-3830 powershell follows symlinks as they do exist in NTFS, and of course in linux

JAL-3830 Powershell wrapper now works cross-platform. Who needs bash?!

JAL-3830 Make wrapper scripts executable

JAL-3830 powershell wrapper tested and fixed

JAL-3830 improved bash scripts. Added powershell script. Needs testing

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    /utils/getdown/jalviewc.ps1
JAL-3830 unix and macos wrappers. Symbolic link to jalviewc-macos in Contents/MacOS/jalviewc.

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    /utils/getdown/jalviewc
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    /utils/getdown/jalviewc-macos
JAL-3830 Improved for .app dir name with spaces, e.g. Jalview Local. Tested on mac to be working.

JAL-3830 install4j adds script to Jalview.app/Contents/MacOS/jalview but we need install4j9 to make it executable

JAL-3830 first draft of wrapper script to go in macOS Jalview.app/Contents/MacOS/jalview

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    /utils/install4j/macos_jalview
Merge branch 'task/JAL-3796_notarization' into develop

Merge branch 'develop' into task/JAL-3796_notarization