Git is a version control system that uses a three tree architecture of the working copy, staging area, and repository. The staging area allows for finer control over commits by staging files before committing them. Branching in Git is lightweight and allows developers to work independently on different versions of code. Merging branches can result in conflicts if the same code sections are modified in different branches. The .gitignore file specifies files that should be ignored and not committed to the repository.