Thats right, minion keeps its own database of what addons are installed:
C:\Users\<Username>\.minion\minion.xml
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The format of this database
<addon md5="efa396d85b290e9c533748f62a3775ac" ui-version="0.5.2" uid="298"/>
md5 - md5 hash for addon archive when it was downloaded.
ui-version - version of installed addon
uid - addon unique id, is same with the id from addon page link http://www.esoui.com/downloads/info298-ShowMotifs.html
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If you want to trigger update, lower the vesion and changes md5(just few characters).
If you manually removed the addon, remove the corresponding lines from that xml.
Also, for a fresh install, you may consider to remove saved variables for the addons you've removed(SavedVariables folder).
Originally Posted by Seroczynski
Yes that works, but it also means that if you ever change something manually outside of Minion it won't get tracked.
By the way, thanks for always taking your time to reply :-)
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