Recommended install procedure :
1. Install JotCache from file com_jotcache_3.x.x_j1X.zip via Administrator > Extensions > Install/Uninstall / Upload Package File.
During installation process are installed both parts of JotCache solution : JotCache component and JotCache plugin. JotCache plugin is during installation set to the last position in order of Joomla system plugins with state disabled.
2. Open Plugin management : Administrator > Extensions > Plugin Manager / in Select type put 'system' and disable 'System - Cache' (when enabled) and open JotCache edit. Set plugin parameters as you like and save it with plugin enabled.
3. Reset the old cache content with Tools > Clean Cache select all items and press DELETE button.
4. When you are using System SEF plugin then JotCache plugin have to follow the System SEF plugin in the Joomla plugin list (adjust order in Extensions > Plugin Manager, the best position for JotCache is the last item in the list)
Simply install new version of JotCache as described in 'Installation' over old one. This procedure applies also in the case when you are upgrading from JotCache version 1.x or 2.x.
With JotCache uninstallation you remove all related database tables, component and plugin files. Uninstallation procedure is following :
1. Uninstall JotCache Component (when installed) : Administrator > Extensions > Install/Uninstall > Components check JotCache and press Uninstall button.
Now are all parts of JotCache removed from the application and database.