I tried to fix it in 5.1.2 but @konste you need to test as well since the relatred bug I fixed for you introduced this issue. So my fix was wrong (tbf it was a shot in the dark) and I'm not sure if now everything is well.

5.1.3 already underway with yet another fix

I will test when 5.1.3 is out.

Gosh... you are too fast for me! Ok, will test now.

PaketPackRepro3.zip
Attached repro shows that simple bin\Release ==> Tools\ causes EXE and PDB duplication (in the same folder!). At the same time adding !bin\Release\*.exe causes both copies of EXE to disappear.
Before jumping on fixing it we need to spend a little time designing what the desired behavior should be and how to make it predictable. Most confusion is coming from the fact that list of files to copy is coming from two sources - dependencies Paket found and explicit list in files section. But negative clauses in the files section affect both sources. Let me think for a few minutes...

That's what I feared. The problem is that for some reason we can't detect that the target is the same. We can definitely detect that the source is the same. But that causes trouble

It almost feels like two sources of files should be independent. First source - dependencies and primary output of the current project is one thing - it should go to the output regardless. Files section should work within itself - it adds some files, then may be exclude some files, but exclusion should only affect what it added!
This way primary output will always go where it belongs and if somebody (like me) wants to take everything else he can add bin\Release ==> Tools\ and !bin\Release\*.exe to add everything but EXE.

@konste in any case we are not allowed to add two files into same folder inside zip. but that is what is happening. trying to fix it

It may sound drastic, but how about we change the logic of taking primary output only to taking everything in the output folder?

doesn't fix the root cause here. maybe it would fix your issue ;-)

For class libraries it would not change anything - they only have DLL and PDB in the output folder. And for other types of projects it really makes sense to take everything as they probably cannot run without the rest of the files anyway.

The problem with the "files" section is that there is no way to tell which part of the project output is primary output and dependencies and which is everything else. It is impossible to author "files" section properly without knowledge what is already included by default. So the algorithm should look like this:

1. Calculate the copy list from primary output and dependencies;
2. Calculate second copy list from the "files" section;
3. Merge the lists removing duplicates comparing target path!

This way whatever curious user writes to the "files" section he or she would only get single instance of all files in each ZIP folder.

see the issue is casing as I expected. Tools vs. tools.

so it can't dedupe it.

Make comparison case insensitive - what's the problem?

other OSes ;-) but yes I guess we need to do that for win.

ok. so I think both are resolved now