AI tools that work on whole code repositories: agents that edit files and write commits, AI review for pull requests, codebase search, and sandboxes for running generated code.
This section is about the repository rather than the single file. The tools here read a whole codebase, change several files at once, write the commit, or review a pull request before a person does. That is where AI assistance saves the most time on real projects, and also where a careless change travels furthest, so how a tool shows you its changes matters as much as what it can do.
Aider works from the command line, edits real files in your repo, shows the diff and creates Git commits. JetBrains Junie runs as an agent inside IntelliJ and other JetBrains IDEs and can run your tests. On the review side, Graphite pairs stacked diffs with AI code review for GitHub, while Sourcegraph Cody answers questions about a large codebase and works with pull-request diffs.
When an agent runs code it wrote itself, run it somewhere that cannot touch production; E2B and Daytona provide isolated sandboxes for exactly that. And whichever tool you use, review its commits the way you would a new colleague's: small, readable and covered by tests.
For help with code inside the editor, see Programming Assistant.