1. Open the documents you want to merge using the Open input files button on the Files tab. Select Folder to open the files in one particular folder (including its subfolders)
2. Go to the Settings tab and check the Binder under Output
3. Go to the Files tab and press the Generate button
4. Select the folder where you would like to save the merged binder
5. Voila!

There are a ton of other options available - you can add stamps, bookmarks and a table of contents.

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You can add additional metadata columns to the document list. The metadata can then be added to stamps, bookmarks and table of contents.

1. In the files tab, with documents loaded, click the plus sign within the square on the right of the document list. Type a name for the new column.
2. Enter the data
3. Switch to the output tab to add the new metadata to your binder
4. To add the new metadata as stamp: Add a new stamp, put the cursor into the text field and click the name of the added column below the stamps list
5. To add the new metadata as bookmark: Put the cursor into the bookmark build string text field and click the name of the added column below the field

If the metadata is already available in the file names or in the bookmarks you can use PdfClerk to extract the information using metadata extraction.

You can also add metadata using Excel.

Adding a metadata column

Adding metadata as stamp

Adding metadata as bookmark

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Documentation bundles become more accessible with clickable links for direct lookup. That is convenient and sometimes also a regulatory requirement like in the case with the MDRs.

The following examples show how to create the documentation bundle provided in the Examples section. The result looks like this.

1. Using the preset selector box in the top right, select & load the “Simple Linking” preset
2. Select Open files > Single file to link and select the word or pdf file containing the checklist (this could be a Word file or a PDF file)
3. Optionally, to control how the links will look, in the Autolink tab uncheck the Underline links option and set the Highlight links color to "#e7f0f4"
4. Under the Settings tab make sure that Binder is selected as output format.
5. Optionally, to add bookmarks, check the Add bookmarks option under the Settings tab
6. Click Generate

All occurrences of filenames referenced in the text in the checklist are transformed into a link to that file. The link links directly to the correct page number if the page number is provided in the text. If the file names in the documentation do not match the way the documents are referenced in the checklist, alternatives may be entered in the Alias text boxes.

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You can add hyperlinks to pdf files from within MS Word using the add hyperlink function (Ctrl+K). This method can be an alternative to PdfClerk’s Autolink feature if the references that you want to transform into links do not follow the same patterns.

When you merge the document containing the links together with the files being linked to using PdfClerk, PdfClerk will recognize that the linked files have been merged in and update the links to point to the document in the bundle.

Example with a letter linking to exhibits:

1. Save the exhibits in a folder
2. Save the letter that you want to link from in the same folder or the parent folder to the exhibits folder
3. Add links from the letter to the exhibits using the add hyperlink link function in MS Word (Ctrl+K)
4. Save the letter as a pdf from Word to the same location as you saved the Word document in step 2
5. Open PdfClerk and select “Open input files”, “Folder” and select the folder containing the letter (which also contains a folder with the exhibits)
6. Click the Generate button
7. Select an Output folder

Additional notes:

• By default Word saves the path to the linked document as an absolute path. In order for PdfClerk to recognize that the link in the letter links to the same exhibit that is merged in, do not move the files before creating the bundle
• Alternatively you can add a “Hyperlink Base” to the word document (Microsoft documentation). Word will then create relative links making it possible to move the letter and the exhibits to another location with the links maintained
• If you ctrl+click on the added links in Word, word will change the color of the link to mark it as visited. This change will be preserved when you save the file as a pdf from word. To reset the color changes, simply close and reopen the document before you save it as a pdf.
• If you add a hash symbol (#) and a page number after the document name in the Word link dialog, PdfClerk will link directly to that page number. (Exhibit 1.pdf#4 - links to page 4)
• If you do not want to bundle the document but still use the direct-to-page links you can process the letter using the Reconnect links in binders function located in PdfClerk’s tool tab on the letter

Once you have loaded a list of documents or a bookmarked binder using the Open Input files, you can edit their names by clicking the name.

Click the icon to the right to remove an item. Select multiple items before clicking the remove icon to remove multiple items.

To manually reorder the items in the document list, select the document or documents you want to change the position of by clicking the circle to the left (1). You can then move the document up or down using the arrows to the left of the document list (2).

Use the shortcut keys to work more efficient:

• Move items by holding down the ctrl-key while using the up or down arrow keys on your keyboard. If you click ctrl+key in combination with the arrow key the item will be moved 10 steps.
• Expand the selection up or down by holding the shift key while pressing the up and down arrow keys on your keyboard.
• Move the selection by holding down the alt-key while pressing the up or down arrow key on your keyboard

You can sort the documents using the sort function.

Each item in the document list has a level. Levels are used in hierarchy for bookmarks, table of contents and folder structures. You can change the level of an item by clicking the arrows next to the level indicator in the document list.

To change the level for multiple items at the same time select multiple items by checking the circles to the right before changing the level.

If the reference you want to link up is identical to the name of the document you want to link to, you can use the function Simple Linking.

This is typically the case if you work with multiple factual abstracts named FA01.pdf, FA02.pdf etc. and you have references like “FA01 p. 3231” etc that you would like to add direct to page links to.

Follow these steps:

1. Make sure the document with the references is converted to PDF and located in the same folder as the factual abstracts (the FAs).
2. Check that the references in the document match the filenames of the factual abstracts, e.g. “FA01” = “FA01.pdf”.
3. Open PdfClerk.
4. Select the Simple linking configuration in the top right corner.
5. Go to the Settings tab and under Output, choose Modified documents.
6. Go to the Files tab, click Open input files, choose Single file to link, and select the document with the references already saved in the folder specified in step 1.
7. Choose a location to save the updated version of the document with Select output folder (not the same folder as in the previous step).
8. Click Generate.
9. PdfClerk will now create a new version of the document and place it in the folder specified in step 7.
10. Move the new file to the folder containing the factual abstracts (folder in step 1) for the links to work.

Use the Update Links function under the Tools tab to change the target of multiple links in a pdf file at the same time. This is handy if the name or location of the target file has changed.

1. Click the Select file button to select the file containing the links to be updated
2. Input the address pattern that the links to be updated starts with.
3. Optionally qualify which links should be updated by selecting a link type in Link types
4. Input the new address pattern that the updated links should start with in the Replacement box
5. Optionally select to convert all matched links to a particular link type by selecting a value for the “Update to” selection.
6. Check the Include bookmarks checkbox to also update matching links in the bookmarks
7. Click Update links

It may be difficult to figure out the exact link addresses for the links in a pdf document. If you do not provide any values for updating the links, PdfClerk will just list the addresses of the links found in the pdf in the log tab. Read more in the documentation.

1. Verify that the reference matches the alias. In its simplest form PdfClerk uses the filenames as alias for the document. Check that the text written in the Alias column in the document list matches the reference in the document exactly. You can configure PdfClerk to ignore case and zero-padding when matching.
2. Check the actual text in the PDF you are adding links to. Open the document in your PDF viewer and copy the text of the reference that is not working (select the text and copy). Paste it into Notepad or some other text editing tool. Check that the text is as expected. If it's wrong and the document is image based (like scanned or similar) run OCR again.
3. Check the log. Go to the Log tab and look for entries in the log that explains why the linking is not working. What does it say? Additionally go to the Settings tab and turn on “Debug” to get additional information (can be quite verbose).

1. PdfClerk adds links with a relative path to the documents. That means that if you have created links to documents in the same folder, the documents also need to be in the same documents as the document with the link you are clicking for the link to work
2. Check the actual link. You cannot do this in Adobe Reader, you will need Adobe Acrobat or the free alternatives Foxit PDF Reader or PDF Exchange. Alternatively, PdfClerk can list all external links using the Update links function in the Tools tab. Check that the target of the link matches the file linked to.