Bubble up return code from run subcommand
[Tr] Fix issue link in APP's epilog
Switch to click for command line processing
Favour click's echo over print

It behaves nicer on poorly configured systems.
Update help formatting to match click's style
Allow setting of common options with envvars

Thanks to click for making this easy.
Use click's built-in version_option option
Use click's builtin test support

Much nicer than all the manual patching.
[Tr] Update click callback to 2.0 signature
Use number of warnings as exit code in fsck
Use click's isolated_filesystem support in tests
Use click's atomic file writing
Switch to click's colourised output