Tried to save all changes into the project-specific settings, but here are the most notable options:

• Editor | Code Style | C/C++ | General
  • C/C++ formatting engine: ClangFormat
• Editor | Code Style | C/C++ | Syntax Style
  • Sort include directives: checked
  • Type of slashes to use in include directives: Use forward slashes
  • Use angle brackets instead of quotes: When possible
• Languages & Frameworks | C/C++ | Order of #includes
  • Only Preserve existing #include groups during a sort is checked
  • Added ^<MyLib.*> just above the ^<.* (thus, below the Header for the current file)
• Optionally Tools | Actions on Save
  • Reformat code: checked

A minimal clang-format file is present with the same include sorting options.

The issue

• Open B.cpp
• CLion warns that the includes are out of order (A.h should be before B.h)
• Sort the includes via the context action
• MyLib/A.h is sorted before MyLib/B.h
• If reformat code on save is enabled, the clang-format immediately sorts it back to the correct MyLib/B.hthen MyLib/A.h order