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How to properly uninstall

mymac:~ meself$ brew doctor
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry and just ignore them. Thanks!

Warning: "config" scripts exist outside your system or Homebrew directories.
`./configure` scripts often look for *-config scripts to determine if
software packages are installed, and what additional flags to use when
compiling and linking.

Having additional scripts in your path can confuse software installed via
Homebrew if the config script overrides a system or Homebrew provided
script of the same name. We found the following "config" scripts:

  /usr/local/munki/munkiwebadmin-config
mymac:~ meself$ locate munki
/Applications/Managed Software Center.app/Contents/Resources/MunkiStatus.app/Contents/Resources/munki.py
/Applications/Managed Software Center.app/Contents/Resources/MunkiStatus.app/Contents/Resources/munki.pyc
/Applications/Managed Software Center.app/Contents/Resources/munki.py
/Library/LaunchAgents/com.googlecode.munki.ManagedSoftwareCenter.plist
/Library/LaunchAgents/com.googlecode.munki.MunkiStatus.plist
/Library/LaunchAgents/com.googlecode.munki.managedsoftwareupdate-loginwindow.plist
/Library/LaunchDaemons/com.googlecode.munki.logouthelper.plist
/Library/LaunchDaemons/com.googlecode.munki.managedsoftwareupdate-check.plist
/Library/LaunchDaemons/com.googlecode.munki.managedsoftwareupdate-install.plist
/Library/LaunchDaemons/com.googlecode.munki.managedsoftwareupdate-manualcheck.plist
/private/etc/paths.d/munki
/private/var/db/BootCaches/85073A52-7A3F-4A63-B0B6-C992C2CAFBC6/app.com.googlecode.munki.ManagedSoftwareCenter.playlist
/private/var/db/receipts/com.googlecode.munki.admin.bom
/private/var/db/receipts/com.googlecode.munki.admin.plist
/private/var/db/receipts/com.googlecode.munki.app.bom
/private/var/db/receipts/com.googlecode.munki.app.plist
/private/var/db/receipts/com.googlecode.munki.core.bom
/private/var/db/receipts/com.googlecode.munki.core.plist
/private/var/db/receipts/com.googlecode.munki.launchd.bom
/private/var/db/receipts/com.googlecode.munki.launchd.plist
/private/var/db/receipts/com.googlecode.munki.munkiwebadmin-scripts.bom
/private/var/db/receipts/com.googlecode.munki.munkiwebadmin-scripts.plist
/usr/local/munki
/usr/local/munki/launchapp
/usr/local/munki/logouthelper
/usr/local/munki/makecatalogs
/usr/local/munki/makepkginfo
/usr/local/munki/managedsoftwareupdate
/usr/local/munki/manifestutil
/usr/local/munki/munkiimport
/usr/local/munki/munkilib
/usr/local/munki/munkilib/FoundationPlist.py
/usr/local/munki/munkilib/FoundationPlist.pyc
/usr/local/munki/munkilib/__init__.py
/usr/local/munki/munkilib/__init__.pyc
/usr/local/munki/munkilib/adobeutils.py
/usr/local/munki/munkilib/adobeutils.pyc
/usr/local/munki/munkilib/appleupdates.py
/usr/local/munki/munkilib/appleupdates.pyc
/usr/local/munki/munkilib/fetch.py
/usr/local/munki/munkilib/fetch.pyc
/usr/local/munki/munkilib/gurl.py
/usr/local/munki/munkilib/gurl.pyc
/usr/local/munki/munkilib/iconutils.py
/usr/local/munki/munkilib/installer.py
/usr/local/munki/munkilib/installer.pyc
/usr/local/munki/munkilib/keychain.py
/usr/local/munki/munkilib/keychain.pyc
/usr/local/munki/munkilib/launchd.py
/usr/local/munki/munkilib/launchd.pyc
/usr/local/munki/munkilib/munkicommon.py
/usr/local/munki/munkilib/munkicommon.pyc
/usr/local/munki/munkilib/munkistatus.py
/usr/local/munki/munkilib/munkistatus.pyc
/usr/local/munki/munkilib/removepackages.py
/usr/local/munki/munkilib/removepackages.pyc
/usr/local/munki/munkilib/updatecheck.py
/usr/local/munki/munkilib/updatecheck.pyc
/usr/local/munki/munkilib/utils.py
/usr/local/munki/munkilib/utils.pyc
/usr/local/munki/munkilib/version.plist
/usr/local/munki/munkiwebadmin-config
/usr/local/munki/postflight
/usr/local/munki/preflight
/usr/local/munki/ptyexec
/usr/local/munki/report_broken_client
/usr/local/munki/supervisor
mymac:~ meself$ 

The reason to uninstall it is that it is incompatible with Homebrew.

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Munki and Managed Software Center are not incompatible with Homebrew. You might be better off describing the specific issues you are seeing.

One known issue is that certain versions of the Homebrew installer recursively change the owner of /usr/bin and contents to that of the user installing Homebrew. For Munki to function properly, /usr/local/munki and contents must have a user of root, group of wheel, and not allow writes to everyone. You can fix the issue that a Homebrew install causes simply:

sudo chown -R root:wheel /usr/local/munki
sudo chmod -R o-w /usr/local/munki
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From: Removing Munki

Removing the client tools:

sudo launchctl unload /Library/LaunchDaemons/com.googlecode.munki.*

sudo rm -rf "/Applications/Utilities/Managed Software Update.app"
#Munki 2 only:
sudo rm -rf "/Applications/Managed Software Center.app"

sudo rm -f /Library/LaunchDaemons/com.googlecode.munki.*
sudo rm -f /Library/LaunchAgents/com.googlecode.munki.*
sudo rm -rf "/Library/Managed Installs"
sudo rm -rf /usr/local/munki
sudo rm /etc/paths.d/munki

sudo pkgutil --forget com.googlecode.munki.admin
sudo pkgutil --forget com.googlecode.munki.app
sudo pkgutil --forget com.googlecode.munki.core
sudo pkgutil --forget com.googlecode.munki.launchd

# reset App Store to pull updates from default Apple servers
sudo defaults delete /Library/Preferences/com.apple.SoftwareUpdate CatalogURL

BTW This gets done in a Terminal.

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