I haven’t hit these issues when using worktrees. But what’s a pain is having to compile from scratch every time, and not carrying over gitignored files.

Worktrees are the obvious pick, and I get why. One command, cheap, and if you're the only one driving, then sharing .git is the point rather than a compromise. I started there too.

An agent in a worktree can reach your hooks, your config, another worktree's stash. Probably not a common problem. But when it does happen you're not debugging your code, you're debugging git, and it's not obvious where to even start looking.

The one that actually bothers me is prompt injection. The agent reads an issue, or a dependency's README, or a web page, and what it's told to do is drop a file in the .git it can already write to. Next time you commit, that runs on your machine as you.

Separate thing - worktrees just get annoying to manage. Can't check out the same branch twice, so you're making up branch names to keep git happy. Every one is another directory to keep track of. Then something goes stale and you're back in git worktree prune.

So has any of it got to you? Or do you hit the annoying parts, shrug, and carry on?

I don't think people use it for isolation, but for what the feature enables in the first place: parallel workstreams

It would be interesting to have a general fix for this in git. Something that more carefully splits the metadata from the working copy, a bit like we used to routinely do with "shadow build trees" with autoconf+make etc.

The parallel trees could have different ownership and access privileges, so that the editable working copy does not require the same filesystem access rights as the metadata tree. The git CLI actions would be performed with the more privileged filesystem role, and it would also have to be audited to make sure it treats all the working copy content as untrusted payload.

For me the most pragmatic way to solve this is in the agent harness layer simply prohibiting commands like git force and others in the settings configuration of your harness of choice with pre tool hooks, its quite easy to setup, obvious ones are prohibiting pushes to main, among others.

Unless someone is building their harness from scratch like you this is a 30sec configuration and you could just save your list of blocked commands with wildcards in a file, and copy paste from one harness to the other.

Please stop writing straw man arguments to sell your product. Worktrees do work as intended for most people. And they work better than your broken homepage.

If you want to properly isolate things, use containers. That's not what worktrees are for.

Do people not know how to write blogs without AI anymore? I enjoy hearing a human's unique voice and miss hearing it when it's abscent.

Git worktrees are a great isolation boundary for _changes_ (especially making changes in parallel on a single machine), but not behavior. If you are trying to actually run autonomous agents securely you need something that lives outside the harness that actually blocks actions in a way that can't be prompted around.

We use nono [1] for this internally, essentially blocking any actions we don't want agents to be able to do without human approval. Our developers can just run `task claude` or whatever their harness is) and it pre-wraps it with our profile that enforces:

- Filesystem: read/write only the worktree plus dev-tooling dirs (Go, Doppler, Graphite caches, git common dir); explicitly no Docker socket and it can't edit its own Claude settings files (so it can't loosen its own permissions).

- Network: outbound only to an allowlist - Anthropic, Doppler, Go module proxies, our dev environments while still allowing binding local dev-server ports.

- GitHub: read anything in the org, and create/edit PRs and push branches - but it cannot merge, close, review, or comment on PRs, delete branches, touch repo settings/secrets, manage auth, or use raw gh api. Those are all "human-only". GitHub tokens are never exposed to the agent; they're injected by a proxy so it can't read or exfiltrate them.

This is great because it is harness agnostic - any developer can use whatever harness they want as long as they port the nono profile to it, as it will enforce all of the above in a way that is not tied to a specific harness implementation

[1] https://github.com/nolabs-ai/nono

If you can't be fucked to write your blog, nobody will be fucked to read it.

I think the first question is what exactly are we trying to preserve by using either worktrees or multiple clones? The answer is: non-pushed changes

So if all you want is to work on index.ts in a separate dir from api.ts then worktrees might work well

If you want to be able to rm -rf one of the dirs without wondering about dependencies then yeah multiple clones makes sense

Either way is a way to avoid using more fragile/finicky workflows like stash and stash pop

tl;dr an agent can still run commands that affects other worktrees

Local agents use worktrees. If you do not trust those (or your own input), then what are you doing?

Why a clone over a worktree? The obvious disadvantage I can see is you dont share your git objects with a clone and for really large repos that becomes an issue

This is quite useful. The title and first paragraph anyway; the rest is fluff. I've actually been trying to solve a problem where I have agents running other agents in worktrees, with the delegated agents contained by jai[0], and the delegating agent would always have to check and reconcile the commits since they get jailed (by design for security). Working on clones instead should resolve that cleanly, as I can relax the .git limitation. I do wish I'd thought it this before.

[0] jai.scs.stanford.edu/