What is your PATH set to when you do which gdb ? Did you try to run the gdb manually (full path) ? Also what are the permissions/ownership of the /usr/local/bin/gdb?
When did the kernel panic happen? While "pkg install gdb" was running? In that case, it is perfectly possible that recently created and written files are not there. At any other time, I would be very surprised if previously existing files vanished.
Certainly not immediately after the (dependent) installation of source-highlight, which was also spoilt; and installation of gdb takes a few seconds. So I seem to be losing more than a few seconds' worth of data.
At any other time, I would be very surprised if previously existing files vanished.
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