Warning when upgrading userland to 12.2 via freebsd-update

Hello,
I've upgraded my workstation from 12.1-RELEASE to 12.2-RELEASE, however second call of freebsd-update (after reboot as utility suggested) printed me some warnings. Does this mean that my system has some inconsistencies? As warnings are all related to /usr/src, I can just delete the directory and install pristine src tarball. But maybe another option exists?

Code:
Installing updates...rmdir: ///usr/src/contrib/llvm/tools/lldb/tools: Directory not empty
rmdir: ///usr/src/contrib/llvm/tools/lldb/source/Plugins/Process: Directory not empty
rmdir: ///usr/src/contrib/llvm/tools/lldb/source/Plugins/InstrumentationRuntime: Directory not empty
rmdir: ///usr/src/contrib/llvm/tools/lldb/source/Plugins: Directory not empty
rmdir: ///usr/src/contrib/llvm/tools/lldb/source: Directory not empty
rmdir: ///usr/src/contrib/llvm/tools/lldb: Directory not emptyInstalling updates...rmdir: ///usr/src/contrib/llvm/tools/lldb/tools: Directory not empty
rmdir: ///usr/src/contrib/llvm/tools/lldb/source/Plugins/Process: Directory not empty
rmdir: ///usr/src/contrib/llvm/tools/lldb/source/Plugins/InstrumentationRuntime: Directory not empty
rmdir: ///usr/src/contrib/llvm/tools/lldb/source/Plugins: Directory not empty
rmdir: ///usr/src/contrib/llvm/tools/lldb/source: Directory not empty
rmdir: ///usr/src/contrib/llvm/tools/lldb: Directory not empty
rmdir: ///usr/src/contrib/llvm/tools/lld/tools: Directory not empty
rmdir: ///usr/src/contrib/llvm/tools/lld/lib: Directory not empty
rmdir: ///usr/src/contrib/llvm/tools/lld: Directory not empty
rmdir: ///usr/src/contrib/llvm/tools/clang/lib/Headers: Directory not empty
rmdir: ///usr/src/contrib/llvm/tools/clang/lib/Driver: Directory not empty
rmdir: ///usr/src/contrib/llvm/tools/clang/lib: Directory not empty
rmdir: ///usr/src/contrib/llvm/tools/clang: Directory not empty
rmdir: ///usr/src/contrib/llvm/tools: Directory not empty
rmdir: ///usr/src/contrib/llvm: Directory not empty
rmdir: ///usr/src/contrib/libc++/src/experimental: Directory not empty
rmdir: ///usr/src/contrib/libc++/src: Directory not empty
rmdir: ///usr/src/contrib/libc++: Directory not empty
rmdir: ///usr/src/contrib/compiler-rt/lib/builtins: Directory not empty
rmdir: ///usr/src/contrib/compiler-rt/lib: Directory not empty
rmdir: ///usr/src/contrib/compiler-rt: Directory not empty
done.
 
As warnings are all related to /usr/src, I can just delete the directory and install pristine src tarball.
Yes, it looks like there's something leftover in your /usr/src. Did you perhaps use subversion or git to fetch/update the source tree? That will cause discrepancies if freebsd-update(8) also wants to manage your source tree.
 
Yes, it looks like there's something leftover in your /usr/src. Did you perhaps use subversion or git to fetch/update the source tree? That will cause discrepancies if freebsd-update(8) also wants to manage your source tree.
Nope, I've used only custom kernels for EVDEV and IPSEC NAT-T, but both of them are in GENERIC now. Will freebsd-update understand that it shouldn't update src anymore if I just delete the directory entirely?
 
Will freebsd-update understand that it shouldn't update src anymore if I just delete the directory entirely?
Also remove src from /etc/freebsd-update.conf:
Code:
# Components of the base system which should be kept updated.
Components src world kernel
 
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