The paclet development preferences page allows you to adjust details of
the paclet system.
To open the preferences,
select Window > Preferences > Mathematica,
and then click the tree expander. This shows
a window such as the following.
In this page you can disable various features of the paclet development system, which would never be necessary except under very extreme circumstances.
Trusting the Documentation Tools Palette
Another feature provided by this preference page is to set up the Documentation Tools palette so that it is trusted by the Mathematica front end. If you click the button labelled Auto-Trust Documentation Palette, you will be asked to confirm that you want to modify the trust path, as shown below.
Confirming will set up the front end so that the Documentation Tools from the Workbench is always trusted.
Setting up the front end to trust the Documentation Tools is a perfectly reasonable thing. The warning exists to protect you from unknown content, but this is known content and is safe. If you want to reverse the setting then you should open the Option Inspector in the Mathematica front end. Here you should switch to global preferences and search for Trusted Path. It should appear similar to the following.
To reset to the default value you should click on the clear button, 
.