Version 4.0.9 has been released, with updated links in the original post. Users of version 4.0.1 or later will receive an automatic update prompt. Users of earlier versions should install over using the EXE file in the release (not the ZIP), but see the warnings in the OP.
This release adds PKCE support, eliminating one of the most painful setup steps and allowing Alpha accounts to use EVEMon fully without developer registration. In addition, Alpha account support has been improved with extra descriptions showing which skills are only trainable on an Omega account. Users who already have client IDs and secrets from previous versions of EVEMon can continue to use them; no re-login should be required in many cases.
Several bugs have also been fixed, thanks again to the community who has reported bugs and contributed fixes.