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I have hundreds of files I want to create an embedded index for and do not wish to do it manually for each one. Is there a way to automate the process of creating the indexes for many pdf files? You can recommend any tool for that.
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You can use an Action in Acrobat Pro to do it. Go to Tools - Action Wizard and create a new Action.
Add to it a Save command (from the Save & Export sub-menu) and then click on Specify Settings underneath it.
In the dialog that opens select Embed Index:
Now simply run the Action on your files. You might have to do it in batches, though, as Acrobat is not very efficient and displays each file before processing it.
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