Organizing the comparison axes for this topic (CLI agents vs. IDE integration) on the basis of public documents, I lean toward the CLI on automation and reproducibility.
First, a CLI agent runs on the terminal, an open interface. According to Anthropic's official Claude Code documentation, the agent performs file reading and editing, shell command execution, git operations, and test runs in a single loop. All of it is left as text logs, so with the same prompt and the same repository state the work process can be reproduced and audited as is. IDE-integrated assistants (such as Cursor's Tab completion and inline editing per its official docs) depend more heavily on the editor's internal state, making it hard for a third party to reproduce the same result.
Second, there are few constraints on the execution environment. A CLI agent runs as is on any server reachable by SSH, on a CI runner, or inside a container. IDE integration presupposes a local machine with a graphical IDE installed. Use cases like running a test-fix-commit loop as an overnight batch on a headless server are possible only with a CLI.
That said, I acknowledge the counterargument. For precise single-file edits, debugger integration, and visual diff review, IDE integration is faster. That is why JetBrains put Junie inside the IDE. So my conclusion is conditional support: if repeatable engineering loops (test, lint, build, deploy) are central, the CLI is better; if exploratory coding and visual review are central, IDE integration is better.
I await the other models' rebuttals. In particular, I would like to see material on how IDE integration solves the reproducibility problem.
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