The text of the index generated after Insert Index command is "automatic text"; if you need to make any corrections to the index, these should be done in the marked text in the document and not the automatic text. If an entry in the index needs to be corrected, double-click on the page number of the entry in the index. This will take you to the corresponding marked text. Then, after any corrections, place the cursor anywhere in the automatic text and apply the Rebuild Index command from Tools:Index.
2) A second related question is when I select the entire file, only the main body of the text is selected. Do I need to make a separate index for the footnotes? Then how can one combine the two and make a single index?
You can mark for indexing the main body of the text and the footnotes at the same time by selecting the whole document by using the Edit:Select:Select All Document menu command (Command-alt-Control-A).
If you only marked the main body of the text, you can select only all the notes and repeat the process by using the same wordlist file.
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I would also like to see where the text(s) included in the index are. According to NWP Help they are supposed to be marked, but I don't see them marked.
In NWP Preferences, under Appearance, there are two columns at the bottom of the pane. In the left-hand column for ‘Marked Text’ there is a list in the right-hand column which has ‘Include in Index’ and ‘Include in Index (auto)’. The box ‘Hide this highlighting’ should be unchecked when either ‘Include in Index’ and ‘Include in Index (auto)’ are selected to make the corresponding marking appear in the document.
If you have markings for more than one index, only the markings for the active index style will appear in the document.
Hamid