Fix digest handling after 5ae680e49

This adds a sha256_fd() and fd support to rsa_verify(). This allows
passing the temporary fd directly to these functions to check
the signature. sha256_file() is now a wrapper around sha256_fd().
(nop) Use proper order to lseek()
Fix coredump in pkg-add.

Do not double free pkg_inst object.
Only consider a new version of pkg exists if a version has been push in the bulk
Disable the function to modify the Terminals title
Initial implementation of repository conflicts.
Implement conflicts file output.
Fix bugs with conflicts detection logic.
Fix bugs in conflicts detection algorithm.
Add the cleanup of conflicts structures.
Cleanup temporary db as well.
Rework conflicts system.

Add emitting of conflicts to a manifest.
Add loading conflicts from a manifest.
Add utility functions to operate with conflicts.
Make conflicts a hash table.
Rework and simplify conflicts detection logic.