I already have a (large bunch) of files and would like to turn them into a project managed by Komodo Edit.
I did a “Project/NewProject”, named the project appropriately, and stored the the komodoproject file somewhere. Now I would like to add all my files to this project. How can I do this? I would expect some menu item like “add directory tree to project”, but there is none.
You can simply copy your existing project files into the new project folder in explorer/finder.
Komodo should pick them up straight away
This means that the komodoproject file has to be in the base directory of my project? I didn’t know this. In this case, I will do it the other way around, move the komodoproject file into my project tree, and put it into .gitignore…
Yep, you’re right! 
The approach I take is to create the komodoproject outside of the source tree and then use the “Add > Existing Folder…” entry from the project’s right-click/context menu to add the folders I want considered to be part of the project.
You’re all over-complicating your setups; but to be fair the project setup is not intuitive - something we’ll be touching on soon.
By default Komodo uses the directory of the project file as your project directory, if you want a different directory then you can simply move or save the project file wherever you wish, then hit Project> Project Preferences and change the Project base directory to whatever you want.
We’ll be introducing a project wizard in Komodo 11, possibly even a bit sooner than that.
@rstewart answered this if you want to setup your project this way. The add folder option is a context menu on your project. Many people don’t like having a Komodo project file or any other external files, unrelated to the actual project, in their project so I can understand this need/want.
This is good to know, as it will allow me to have the project file itself outside of the source tree while still referencing the project’s primary directory structure as the “base directory”. I still end up using the “add existing folder” approach to include other folders outside of the project’s folder structure (e.g., folders with shared code and shared assets used by multiple projects). So, instead of having three of these external existing folders – one of which is the project’s primary folder – I can get away with just two.
This seems to imply that I cannot have files in a single project unless they are in the same directory (or at least the same directory tree)?
That is certainly what that sounds like but no that is not the case. You can have project files anywhere on your computer. See @nathanr’s answer above:
and also my own:
Please tell me how I can add a file (other than in the directory) to a project. I have yet find the keystrokes.
Sorry to be dense, but has taken me a long time to find it… Open Projects in left nav; double-click on desired project; right click on same project > Add > Existing File. (Plus right click > Save Project)
I think that Project Wizard that should be introduced in Komodo 11 will resolve this issue 