snapcraft "stage: [ -f ] " causes FileNotFound on second run

I have a snapcraft with two parts, one "copy" and one "cmake". I am debugging files used in the "copy" part.

$ snapcraft clean -s build wrapper && snapcraft --debug

My yaml has

----

parts:
  wrapper:
    plugin: copy
    files:
      dekkowrapper: dekkowrapper

  dekko:
    plugin: cmake
    source: https://git.launchpad.net/dekko
    source-type: git
    ...
    stage:
      - -usr/share/pkgconfig/*.pc

----

First run, snapcraft runs normally. Then I clean the copy part and run again.

$ snapcraft clean -s build wrapper && snapcraft --debug
Cleaning priming area for wrapper
Cleaning staging area for wrapper
Cleaning build for wrapper
Skipping pull desktop/qt5 (already ran)
'dekko' has prerequisites that need to be staged: desktop/qt5
Skipping pull desktop/qt5 (already ran)
Skipping build desktop/qt5 (already ran)
Skipping stage desktop/qt5 (already ran)
Skipping pull dekko (already ran)
Skipping pull wrapper (already ran)
Skipping build desktop/qt5 (already ran)
'dekko' has prerequisites that need to be staged: desktop/qt5
Skipping pull desktop/qt5 (already ran)
Skipping build desktop/qt5 (already ran)
Skipping stage desktop/qt5 (already ran)
Skipping build dekko (already ran)
Preparing to build wrapper
Building wrapper
Skipping stage desktop/qt5 (already ran)
'dekko' has prerequisites that need to be staged: desktop/qt5
Skipping pull desktop/qt5 (already ran)
Skipping build desktop/qt5 (already ran)
Skipping stage desktop/qt5 (already ran)
Skipping stage dekko (already ran)
Staging wrapper
Skipping prime desktop/qt5 (already ran)
'dekko' has prerequisites that need to be staged: desktop/qt5
Skipping pull desktop/qt5 (already ran)
Skipping build desktop/qt5 (already ran)
Skipping stage desktop/qt5 (already ran)
Priming dekko
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/snapcraft/internal/common.py", line 187, in link_or_copy
    os.link(source_path, destination, follow_symlinks=False)
FileNotFoundError: [Errno 2] No such file or directory: '/home/cmiller/work/canonical/snaps/dekko/stage/usr/share/pkgconfig/iso-codes.pc' -> '/home/cmiller/work/canonical/snaps/dekko/prime/usr/share/pkgconfig/iso-codes.pc'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/bin/snapcraft", line 31, in <module>
    snapcraft.main.main()
  File "/usr/lib/python3/dist-packages/snapcraft/main.py", line 202, in main
    return run(args, project_options)
  File "/usr/lib/python3/dist-packages/snapcraft/main.py", line 258, in run
    lifecycle.snap(project_options, args['<directory>'], args['--output'])
  File "/usr/lib/python3/dist-packages/snapcraft/internal/lifecycle.py", line 256, in snap
    snap = execute('prime', project_options)
  File "/usr/lib/python3/dist-packages/snapcraft/internal/lifecycle.py", line 98, in execute
    _Executor(config, project_options).run(step, part_names)
  File "/usr/lib/python3/dist-packages/snapcraft/internal/lifecycle.py", line 127, in run
    self._run_step(step, part, part_names, dirty, recursed)
  File "/usr/lib/python3/dist-packages/snapcraft/internal/lifecycle.py", line 165, in _run_step
    getattr(part, step)()
  File "/usr/lib/python3/dist-packages/snapcraft/internal/pluginhandler.py", line 391, in prime
    _migrate_files(snap_files, snap_dirs, self.stagedir, self.snapdir)
  File "/usr/lib/python3/dist-packages/snapcraft/internal/pluginhandler.py", line 673, in _migrate_files
    common.link_or_copy(src, dst, follow_symlinks=follow_symlinks)
  File "/usr/lib/python3/dist-packages/snapcraft/internal/common.py", line 189, in link_or_copy
    shutil.copy2(source, destination, follow_symlinks=follow_symlinks)
  File "/usr/lib/python3.5/shutil.py", line 251, in copy2
    copyfile(src, dst, follow_symlinks=follow_symlinks)
  File "/usr/lib/python3.5/shutil.py", line 114, in copyfile
    with open(src, 'rb') as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: '/home/cmiller/work/canonical/snaps/dekko/stage/usr/share/pkgconfig/iso-codes.pc'

ProblemType: Bug
DistroRelease: Ubuntu 16.04
Package: snapcraft 2.12.1
Uname: Linux 4.5.0-040500-generic x86_64
ApportVersion: 2.20.1-0ubuntu2.1
Architecture: amd64
CurrentDesktop: GNOME
Date: Tue Jul 19 02:49:59 2016
EcryptfsInUse: Yes
PackageArchitecture: all
SourcePackage: snapcraft
UpgradeStatus: No upgrade log present (probably fresh install)