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When a list is sorted normally, all Categories (i.e. text enclosed in square brackets, not normally exported with Keywords) are also re-ordered with their child-text. Use this button if you want to fix the current position of all categories so that they won't be moved during an alphabetical sort procedure. The 'Fix Categories' tool will lock the current category positions by prefixing numbers to all Category text, within the square brackets. All child-text and lines not enclosed in square brackets will be left un-touched.
The easiest way to explain this is to see it in action. Click 'Tools > Testing' and load the 'Test List with Multiple Categories'. Click 'Tools > Sort > Sort Complete List', and you will see that lots of category lines are moved about, so they are now in alphabetical order. Next, reload the 'Test List with Multiple Categories', then click 'Tools > Edit > Category Positions > Fix Categories'. See how numbers are added to each category, dependent on the indent-level. Now, repeat the Sort, and see that nothing is re-ordered.
If a list has had the current position of all categories fixed using the 'Fix Category Positions' tool, the 'Un-Fix Category Positions' button will remove them. It does this by removing all text before the first space in a category, so if you altered the numbers yourself, be sure to leave a single space before the category text that you wish to remain untouched.