PDFOutliner, PDFoo and PDFExplode are now available for purchase outside the Mac App Store. As a launch special, the three apps are available for 50% discount when purchased together in the "Productivity PDF Bundle" offered by Paddle (US$6.50, offer ends November 27, 2013.)
Also, you can now download fully-functional 7-day trial versions of all three apps on the Downloads page.
PDFCombo is an app to combine multiple PDF files. Unlike other apps, PDFCombo preserves the Table of Contents (TOC) in the combined PDF. It can also add a new top-level TOC entry for each contributing PDF. This can be useful to keep a complex TOC neat & tidy, or to add a TOC item to demarcate contributing PDFs.
For example, if you've created PDFs using the File > Print... dialog in Mac OS X or you've got several scanned PDFs, you can combine them into one PDF with PDFCombo with automatic TOC entries to mark the first page of each contributing PDF.
PDFCombo is a free app available on the Mac App Store.
For editing the TOC in any PDF, consider PDFOutliner.
See also notes to PDFCombo 1.0.2 (published 04/21/2014) and PDFCombo 1.0.3 (published 05/15/2014.)
[2017 Update]: PDFSpeech is a new powerful app that can combine multiple PDF files into a PDF Pack. See this short walkthrough on how to print an entire book from safaribooksonline.com to PDFSpeech to create a PDF with a table of contents. PDFSpeech also includes the ability to insert clipboard contents as PDF into the Pack, and multiple pages selected & copied from Preview. The primary use of PDFSpeech is to help you read more by tapping into text-to-speech technology, and it enables easy control over pronunciations so you can listen to the generated speech for extended periods without any glaring mistakes.
Use PDFoo to create links into a PDF - to chapters, to sections, to pages, and even point on a page. Arrange these links in a mindmap for quick lookups. In this example, the mindmap is created using Mindnode Pro (a excellent lightweight app with iCloud integration). Any application that supports rich text notes also supports PDFoo URLs - applications such as Evernote, Curio, DevonThink, NoteShare, Together, VoodooPad, Scrivener and more. You can even embed pdfoo URLs on a web page (such as a blog post or wiki page) and Safari will faithfully launch PDFoo upon request.
When you are editing the table of contents (TOC) manually in PDFOutliner, you have the option to either refer to pages using page labels (the numbers in red boxes on each page and below the thumbnails) or using the page numbers printed on each page. The video below shows how to use the "p" prefix for printed page numbers.
PDFOutliner has a new application icon!
PDFOutliner now provides several techniques to edit the Table of Contents (TOC) in your PDF.
The Editing Features Overview document (PDF, 0.2MB, 8 pages) goes into the details.
The PDFoo app is meant to help you link into your collection of PDFs.
Each PDFoo URL is a link to a specific page (and position on the page) in a PDF. You can store these pdfoo URLs like any other rich text, such as in a note-taking app like TextEdit, Evernote, DevonThink, NoteShare, Mail.app etc. PDFoo URLs behave like http: URLs. When you have a http: URL in your notes, and you click it, then Safari app opens that URL. Similarly, when you click on a pdfoo: URL in your notes, the PDFoo app opens the correct PDF and scrolls to the correct page and location. In this analogy, every PDF is like a website, and every page in the PDF is like a page on that website.
Here is the workflow: Open the PDF you want to link into. Set the prefix for this PDF (which acts like a web server address). Next, you can create PDFoo URLs in following ways:
(1) select TOC items and drag into scratchpad, or copy-paste
(2) select any text on PDF page and drag into scratchpad, or copy-paste
(3) use the search toolbar button on top-right to search, and drag into scratchpad
(4) use the File > Export Annotations command to extract only the highlighted text and note annotations
(5) double-click anywhere on the page, a bullseye will appear, and keep mouse down & drag into scratchpad
The last technique allows you to link to a very precise location on the PDF page.
Use the above methods to build up your notes with links into the PDF.
Now, you have lots of text and pdfoo URLs in the scratchpad area. Copy-paste the entire notes into Evernote, TextEdit, DevonThink, NoteShare, Mail.app, your website or any other rich-text app on Mac OS X, for safe-keeping your notes. When you need it, find your note and click on the pdfoo: URLs to have the PDFoo pull up the precise page of the PDF.
For example, the following notes snippet has pdfoo URLs that point to 3 separate pages inside a "SEEP Framework Manual (1MB, 123 pages)", and allow me to quickly jump to the specific definition. I assigned the prefix "seep.manual" to this PDF. All the pdfoo URLs were generated automatically by PDFoo when I copy-paste text from the PDF.
Be careful to distinguish between “Impairment Losses on Loans” and “Provision for Loan Impairment” seep.manual/Sec1:124/ which are both from the income statement. They should be read in conjunction with the balance sheet item “Impairment Loss Allowance” seep.manual/Sec1:130/. The relationship with the “Value of Loans Written Off” is explained in Box 2.4. How Financial Statements Are Linked seep.manual/Sec1:148/
I build up these notes in the scratchpad area as I browse the PDF, and when done, I save it inside Evernote for long-term access. When I want to refer to this content next time round, I pull up the note in Evernote and click on these links inside Evernote, and PDFoo opens up the PDF and scrolls to the correct location for that link.
Moreover, the pdfoo URL feature can be used to build a TOC for the PDF outside the PDF. For example:
Conventions used in the manual seep.manual/Sec1:115/
Table 2.2. Income Statement Detail seep.manual/Sec1:123/
Table 2.4. Balance Sheet Detail seep.manual/Sec1:130/
Table 2.5. Classification of Cash Receipts and Payments seep.manual/Sec1:134/
Table 2.7. Direct Cash Flow Statement Detail seep.manual/Sec1:137/
Table 2.9. Indirect Cash Flow Statement Detail seep.manual/Sec1:141/
Table 2.11. Portfolio Report Detail seep.manual/Sec1:144/
Table 2.13. Non-Financial Data Report Detail seep.manual/Sec1:146/
Table 3.1. Summary of Adjustments seep.manual/Sec1:150/
Save these sort of links inside Evernote (or other note-taking fast-searching app) and you can quickly jump to any important location in your PDFs.
Workflow for annotating PDFs
Skim.app is a free, open source Mac OS X app which is great for annotating PDFs. In particular, the Text Note tool provided by Skim (shortcut CTRL CMD 1) allows you to draw "sticky notes" on a PDF page and write comments. Skim does not modify the original PDF directly, and annotations are kept in extended attributes, i.e. hidden information attached to the PDF file on disk. To ensure that these annotations do not get clobbered when syncing PDFs via Dropbox or a similar application, make sure to turn on "Automatically save Skim notes backups" option in Skim Preferences. This will create a small-sized .skim file adjacent to the original PDF to hold all the Skim-created annotations. This is a reliable way to annotate a PDF on multiple computers using Skim, since only the small-sized .skim file has to be synced across computers.
Export PDF Annotations with PDFoo
Skim can export a new PDF with embedded notes (i.e. annotations) using the File > Export menu command. Open this new PDF using PDFoo, and export annotations with pdfoo:// URLs that provide a context for each note and allow you to jump back to the source PDF.