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QPDF is a C++ library and set of programs that inspect and manipulate the structure of PDF files. It can encrypt and linearize files, expose the internals of a PDF file, and do many other operations useful to end users and PDF developers.

pdfcrack is a command line, password recovery tool for PDF-files.

PDF Chain is a graphical user interface for the PDF Toolkit (PDFtk). The GUI supports all common features of the command line tool in a comfortable way.

The PoDoFo library is a free, portable C++ library. It can parse and modify existing PDF files and create new ones from scratch. It also includes several tools to work with PDF files. It features an unique approach which provides access to PDF documents via an object tree. Therefore, PDFs can be created and or manipulated using a simple tree structure. Development of PoDoFo has been moved to GitHub: https://github.com/podofo/podofo Please raise new issues in the GitHub project.

Free editor for PDF documents. Complete editing of PDF documents is possible with PDFedit. You can change raw pdf objects (for advanced users) or use many gui functions. Functionality can be easily extended using a scripting language (ECMAScript).

Cross-platform command-line tool for creation of PDF documents from scans/photos of pages in JPEG (.jpg) format and the lightest weight ANSI C library to put multiple JPEG files into one PDF file. You can add handwritten comments to PDF scans (over original images) with xournal: http://xournal.sourceforge.net/ It supports graphics tablets and saves comments to PDFs as vector data.

iText is an open-source PDF library available for Java and .NET (C#). iText allows you to effortlessly generate and manipulate standards-compliant PDF documents with a powerful and feature-rich SDK. With iText, you can create archivable and accessible PDFs, split and merge documents, fill and flatten forms, digitally sign documents, and more. iText add-ons enable additional functionality, such as PDF creation from HTML templates, secure redaction, OCR, and much more.