Combining PDF files into one with PDF by Zaweba
Join PDFs into one document with a bookmark per file, interactive form fields, layers, links and attachments kept, and shared fonts stored once.

Joining PDFs sounds like the simplest job going: take the pages of several files and put them one after another. In practice, a lot can go wrong. Form fields stop working, links point nowhere, file sizes balloon because the same font is stored ten times, and the result is one long scroll with no way to find where each original began.
PDF by Zaweba's File > Combine files is built to avoid those problems. It joins files object by object rather than page by page, keeps what makes each document work and gives the result a bookmark for each file you added.
Building the list
Combine files opens a list. Add files from disk, or add documents you already have open in tabs. Remove any you added by mistake, move them up and down, or sort them by name, which is handy when files are numbered or dated in their names.
Each file has its own page list, so you do not have to take every page. That is useful when you want just the signed page from one document and the whole of another. You can also show files as thumbnails, which helps when several have similar names. A file-size choice is offered too, for when the result needs to travel by email or upload.
When you combine, the result opens as a new, unsaved document. Nothing is written over your originals, and you decide where the combined file goes when you save.
What is kept
This is where joining object by object matters. Form fields stay interactive, so a combined set of application forms can still be filled in. If two files have fields with the same name, they are either renamed, so the second becomes name_2, or merged into one field.
Layers are kept, along with links, named destinations and attachments. Tags from each file become one tag tree, which keeps the structure that screen readers and other tools rely on. Fonts and pictures shared between files are stored once rather than repeated, which keeps the file size down.
And every file gets its own bookmark. Open the bookmarks and you can jump straight to the start of each part, which makes a combined pack far easier to read.
Combine, check, save
Gather the files and decide the order before you start. Naming them with a number at the front, then sorting by name, saves dragging things about.
Combine, then go straight to the Organise pages grid and look over the result. Check the first page of each part, look for blank pages and make sure nothing landed sideways. If the parts had their own numbering, set page labels so the on-screen numbers match.
Then fill in a field or two and click a few links to check they work, and save under a clear new name.
Where combining fits
Combining is often the middle of a bigger job. You might make PDFs from pictures or text files first, combine them into one pack, add comments or stamps, then export or print. Because everything happens in one offline app, the whole chain runs without uploading anything.
It also pairs well with page tools. If the files come in different paper sizes, Change page size can bring them into line afterwards.
Things to watch
Same-named form fields are the main thing to check. If the files are copies of the same form filled in by different people, make sure the answers stay separate after combining.
Keep the originals. The combined document is new and unsaved, so your source files are untouched, but it is still wise to keep them until you are happy with the result.
Done this way, combining gives you one tidy, working document rather than a heap of pages stuck together.