You are using the text editor. If you care about NULs, trailing EOLs and (possibly) conflicting encodings, should you still use a hex editor?
If I need this amount of control over my operations, I use the xxd route really, with
:se binary
One nice option that you seem to miss is inserting the register of the insert expression:
Cr =system('ls -l') Enter
It may or may not be smarter / less intrusive in the character encoding business, but you can try it if it's important enough for you.
Or you can use Perl or Python support to use popen effectively
Tough idea:
:perl open(F, "ls /tmp/ |"); my @lines = (<F>); $curbuf->Append(0, @lines)
sehe
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