A free demo version of this tool that will combine up to two files in each folder can be found here.

This is a new batch tool, so it can only be used in Acrobat Pro.
With this tool you can combine all of the (PDF) files in a folder to a single file (in order!) and have this file saved into the same folder (using the folder's name as the new file name).
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New feature: You can now select to automatically create a bookmark pointing to each file in the merged document.
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ANOTHER new feature: Now you can also select to create a single, "master" file at the end of the process, which contains all of the processed files, including a bookmark for each folder and file.



So if you have the following folder structure:

- \Root
- 1.pdf
- 2.pdf
- 3.pdf
- \SubFolder1
-- 4.pdf
-- 5.pdf
- \SubFolder2
-- \SubFolder3
--- 6.pdf
--- 7.pdf
-- 8.pdf
-- 9.pdf

The script will create 3 combined PDF files: files 1 to 3 will be saved as Root.pdf in the root folder; files 4 to 5 will be saved as SubFolder1.pdf in SubFolder1; files 6 to 7 will be saved as SubFolder3.pdf in SubFolder3; and files 8 to 9 will be saved as SubFolder2.pdf in SubFolder2.

Here's another example:
We have a folder called "Placeholder 3" under C:\Temp\Forms\.

We run the batch on "C:\Temp\Forms" and select to create a bookmark for each file (excluding the ".pdf" extension).

The result is a single file, called "Placeholder 3.pdf".

This file is the result of all the single files in that folder, including the bookmarks we wanted to create.

After the individual files have been combined, you can create the "master" file:

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