usrmerge handling is not dealing with subdirectories

[tigarmo]

Our code that archives the lifecycle payload as a new layer is taking the usrmerge into account when handling files, but not when handling subdirectories; So for example, if a part primes two files:

- bin/f1
- lib/subdir/f2

bin/f1 will be correctly archived as usr/bin/f1, but lib/subdir/f2 will stay as lib/subdir/f2, possibly breaking the usrmerge symlink (depends on the version of... something).

Here's a rockcraft.yaml that repros this:

name: usrmerge-dir-bug
base: ubuntu:22.04
version: '0.1'
summary: usrmerge-dir-bug
description: usrmerge-dir-bug
license: GPL-3.0 
platforms:
  amd64:

parts:
  p1:
    plugin: nil
    override-build: |
      cd ${CRAFT_PART_INSTALL}

      mkdir bin
      touch bin/f1

      mkdir -p lib/subdir
      touch lib/subdir/f2

Building it and then loading it in dive shows the issue; see on the right the lib entry has no permissions - that's the tell that it's broken:

The build log shows it too:

2023-02-07 16:02:11.359 :: 2023-02-07 19:02:10.607 Creating new layer
2023-02-07 16:02:11.359 :: 2023-02-07 19:02:10.608 Skipping /root/prime/bin because it exists as a symlink on the lower layer
2023-02-07 16:02:11.359 :: 2023-02-07 19:02:10.608 Adding to layer: /root/prime/bin/f1 as 'usr/bin/f1'
2023-02-07 16:02:11.359 :: 2023-02-07 19:02:10.614 Skipping /root/prime/lib because it exists as a symlink on the lower layer
2023-02-07 16:02:11.359 :: 2023-02-07 19:02:10.614 Adding to layer: /root/prime/lib/subdir
2023-02-07 16:02:11.359 :: 2023-02-07 19:02:10.615 Adding to layer: /root/prime/lib/subdir/f2 as 'lib/subdir/f2'

[tigarmo]

fixed by #200