The 6.x-2.x branch is the only actively developed branch. Please see INSTALL.txt for details on how to setup the module.
Click Heatmap 3.x Major Changes
The 3.x lines of development (both for D6 and D7) utilize the Libraries API. If you are so brave and bold as to run the [6|7].x-3.x-dev code, you *must* move the clickheat library you downloaded when you first installed the module out of the module's directory (sites/all/click_heatmap/clickheat) to the libraries directory (sites/all/libraries/clickheat.)
The "count clicks" permission has been inverted to "ignore clicks." This makes more sense as most sites want to see what the users consider to be the most important, and filter out the work of content creators and administrators. This means that User 1 never gets counted. If you're configuring the site as User 1 and don't see any data, that's why.
The 3.x branch of the module allows the admins to select which pages to track clicks in a familiar manner, because it was lifted straight from the blocks module. The update hooks will automatically convert settings from the old "scope" control to the "new" format.