Hi, Gothboy -
The official procedure -
Article #10182 - Rebuilding Desktop File
The procedure I use... To rebuild the desktop safely, restart - immediately hold down the Shift key until you get the "Extensions Off" message; then release Shift and hold down the Command and Option keys until you get the splash screen asking if you want to rebuild the desktop; click yes (or okay). Once that's done, restart to turn your extensions back on.
<hr>
The label that heads each column in Extensions Manager is actually a button. For most of the columns, it allows changing the sorting criterium - for example, if you click the "Package" button, it will sort the items by the info in the package column, handy for when trying to locate all items that came with a ceretain package.
The label atop the leftmost column is named "On/Off" - clicking that will turn all items on or off; you may need to click it twice to get to the status you want. Note, though, that after rebuilding you would then need to return all items to their original status one by one, manually - not a fun thing to do.
You can create a text file of what is on and what is off by selecting the Save Set as Text item in the File menu, and use it as a guide to turn selected items back on.
Or, create a special set just for rebuilding - click the Duplicate Set button, name the new set something appropriate, make sure it is active, then disable all the ones you want to be off during desktop rebuilding. Then all you need do is switch to that set, restart and rebuild the desktop, then switch back to your regular set and restart again.
Since I'm a lazy person, I prefer to just start up with Extensions Off using the Shift key - does what I need with no messing with individual extensions.