file-root is not updated / has old leftovers

Description of Issue/Question

I'm trying to run a state.show_highstate from the local files cache but it fails with conflicting ids due to old cached files.

# /usr/bin/salt-call --local --file-root=/var/cache/salt/minion/files/base/ --pillar-root=/var/cache/salt/minion/pillar/ state.show_highstate
local:
    - Detected conflicting IDs, SLS IDs need to be globally unique.
          The conflicting ID is '/var/qmail/alias/.qmail-ph-otrsqueue' and is found in SLS 'base:service.mail.aliases' and SLS 'base:pkg.qmail.aliases'

If i delete the cache /var/cache/salt/minion/files/base issue a state.apply and try again everything is fine.

A diff afterwards of the old base dir and new base dir shows:

# diff -upr base_old/ /var/cache/salt/minion/files/base/
Only in base/_macros: default_settings.sls
Only in base/_macros: host_settings.sls
Only in base/_macros: role_settings.sls
Only in base/_macros: settings.sls
Only in base/_returners: flasticsearch.py
Only in base/: config
Only in base/install: kernel_reboot.sls
Only in base/install: reboot.sls
Only in base/: ph
Only in base/pkg: btrfs-tools.sls
Only in base/pkg/jailinst: config.sls
Only in base/pkg/jailinst: default_shelllimits.yml
Only in base/pkg/jailinst: init.sls
Only in base/pkg/linux-image: is_supported_and_secure.sls
Only in base/pkg: linux-image.sls
Only in base/pkg/logrotate/files: logrotate
Only in base/pkg: os_base.sls
Only in base/pkg: roundcubemail-ph.sls
Only in base/pkg/salt-minion/files: ph-elastic.conf
Only in base/pkg/salt-minion/files: ph.conf
Only in base/pkg/salt-minion/files: salt-minion.conf
Only in base/pkg/salt-minion/files: salt-minion.service
Only in base/pkg/salt-minion: restart.sls
Only in base/pkg: salt-minion.sls
Only in base/pkg: servercon
Only in base/pkg/systemd/files: timesyncd.conf
Only in base/pkg/systemd/files: timesyncd.conf.jinja
Only in base/pkg: toolkit-ph.sls
Only in base/pkg: zabbix-agent-ph.sls
Only in base/pkg: zabbix-agent.sls
Only in base/repo: apt-update-bug-38090.sls
Only in base/repo/files: ph.pub
Only in base/: run
Only in base/service: mail
Only in base/service: salt
Only in base/service: ssh
Only in base/service: tuning
Only in base/service: zabbix-agent
Only in base/setup: salt_git_deploy_key
Only in base/: startup_states

Versions Report

# salt-call --local --versions-report
Salt Version:
           Salt: 2017.7.4
 
Dependency Versions:
           cffi: Not Installed
       cherrypy: Not Installed
       dateutil: 2.5.3
      docker-py: Not Installed
          gitdb: Not Installed
      gitpython: Not Installed
          ioflo: Not Installed
         Jinja2: 2.9.4
        libgit2: Not Installed
        libnacl: Not Installed
       M2Crypto: Not Installed
           Mako: Not Installed
   msgpack-pure: Not Installed
 msgpack-python: 0.4.8
   mysql-python: Not Installed
      pycparser: Not Installed
       pycrypto: 2.6.1
   pycryptodome: Not Installed
         pygit2: Not Installed
         Python: 2.7.13 (default, Sep 26 2018, 18:42:22)
   python-gnupg: Not Installed
         PyYAML: 3.12
          PyZMQ: 16.0.2
           RAET: Not Installed
          smmap: Not Installed
        timelib: Not Installed
        Tornado: 4.4.3
            ZMQ: 4.2.1
 
System Versions:
           dist: debian 9.4 
         locale: UTF-8
        machine: x86_64
        release: 4.12.0+147-ph
         system: Linux
        version: debian 9.4 

Start by reproducing the local state.show_highstate command with the reported --file-root and --pillar-root, then compare the cached files before and after state.apply. Investigate how Salt 2017.7.4 updates /var/cache/salt/minion/files/base/; done means stale files no longer cause conflicting IDs in the highstate output.