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PDFCraft is an extensible toolkit for creating, editing, and transforming PDF documents with both a graphical interface and a scripting API, making it useful for users ranging from casual editors to automated document processors. At its core, the project provides a clean, modern UI where you can rearrange pages, annotate text, insert images, fill forms, and export to multiple formats, all without needing a heavyweight commercial PDF suite. But beyond manual editing, it also offers a...

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.

Split and merge PDF files with PDFsam, an easy-to-use desktop tool with graphical, command line and web interface.

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.

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.