How do I do the initial setup of the BitBucket SourceTree project?

Question

git

Hello !
Please tell me the algorithm of actions for the initial setup of the working copy of the git project in the BitBucket SourceTree.
There is a git web project, but a lot of necessary files (frameworks, cache, and much more) are not included in the project, although they are available directly on the server. For convenient work, I want to run the project on a local machine and commit from it as needed.
Try once.
The current version of the project was downloaded via FTP and installed on a local server. When trying to clone to the BitBucket project folder, SourceTree reported that there were files in the target folder, which, in its opinion, was the reason for the refusal of the operation.
Attempt Two
Tried to add a repository, getting rejected with the form "Repository type: This is an invalid working copy path".
Attempt 3, most successful
An empty project folder has been created. Project files have been successfully cloned into this folder. Then the "missing" files from the combat server were added. But the suggested files for indexing reflect all changes to the project folder. Ignoring directories seems to be a good way to solve problems, but not ideal. A huge number of folders and the presence of intersecting paths is a titanic work.
Is there a way to gracefully get out of this difficult situation for me?