The Claude Code folder

The Claude folder is where Claude Code keeps its configuration: rules, skills, commands, agents, CLAUDE.md, and settings.json. It’s exactly what KoNiMa Claude Sync reads from this machine and writes back to when something arrives from the others. By default it lives in ~/.claude, inside your home folder.

In the vast majority of cases you don’t need to do anything: Claude Sync finds it on its own. This page explains what happens when the folder is elsewhere, when it’s missing, or when you have more than one.

My folder is in a non-standard place — how does it find it?

Claude Sync decides which folder to use by following a precise order, stopping at the first one it finds:

the Claude folder setting, if you filled it in by hand;
the CLAUDE_CONFIG_DIR environment variable — Claude Code’s own official override — which is detected automatically, with no prompt;
the default ~/.claude.

Anyone who keeps their configuration in a non-standard place has usually already set CLAUDE_CONFIG_DIR to make Claude Code itself work: in that case detection is automatic and you have nothing to configure in Claude Sync.

The Claude folder setting applies to this machine only and never travels: it’s a local choice, not part of the shared configuration. A relative path in the setting is ignored, and detection falls back to automatic.

Does Claude Sync ask me which folder to use?

Only when it genuinely can’t tell them apart. If this machine has more than one real Claude Code folder — for example a personal ~/.claude and a company one reached through CLAUDE_CONFIG_DIR — Claude Sync asks you which one to sync instead of guessing and binding your repository to the wrong one. See I have more than one Claude folder below for exactly when and how.

In every ordinary case — a single folder, or one you’ve already chosen — it says nothing and simply gets on with it. It never interrupts you with a random popup.

You can still choose the folder by hand at any time with the Choose folder… button, which appears in a single place: the Claude folder row of the System check (System tab), and only when that check isn’t OK. The folder you pick is validated: it must contain recognizable Claude Code configuration. If you pick the wrong folder, it’s rejected with a message along the lines of “That folder does not look like a Claude Code folder — it has no settings.json, CLAUDE.md, skills or agents. Nothing was changed.”

If instead the folder is valid and you confirm, the change is immediate: Claude Sync restarts itself on the new folder, without reloading the editor and without re-cloning anything. If you cancel, nothing changes.

What if the folder is wrong or missing?

When the folder is missing, empty, or likely not the right one, Claude Sync says so openly instead of showing a false “everything synced”:

the status bar turns yellow with a warning icon and is never green;
every dashboard tab shows the Claude folder not found banner, with the path where the app is looking;
the summary state reads the Check setup pill.

The Claude folder row of the System check spells out exactly which case you’re in:

Verdict	What it means
Missing	Your Claude Code folder was not found at this path — there is nothing to sync from or to.
Wrong place	Claude Code is set up on this machine but not in this folder — Claude Sync is looking in the wrong place.
Empty, but the repository has content	This folder holds no Claude Code configuration, but your repository does — Claude Sync is reading the wrong folder.
Genuinely fresh machine	No Claude Code configuration here yet — the first sync will create it.

Claude Sync never creates the folder itself, with a single exception: a genuinely fresh machine where Claude Code has never run, where the first sync creates it as expected.

The System check modal: each environment row with a status icon; the Claude folder row is flagged, showing its verdict and a Choose folder… button The System check, with the Claude folder row flagged and the Choose folder… button that fixes it.

I have more than one Claude folder

Some machines carry two genuine Claude Code installations at once — a personal ~/.claude and a company one reached through CLAUDE_CONFIG_DIR, or a second ~/.claude-work alongside the default. When Claude Sync finds two or more folders that actually contain Claude Code configuration and you haven’t chosen one yourself, it asks you which to sync rather than guessing — because the folder it picks is the one your repository is bound to, and a wrong guess would tie the sync to the wrong profile.

During first setup (before a repository is connected) the question comes first: “Claude Sync found more than one Claude Code folder on this machine. Choose the one to sync — your repository will be set up in the folder you pick.” Each candidate is labeled by where it came from — default folder, set by CLAUDE_CONFIG_DIR, or found on this machine — and you pick one with Use this folder (or Browse another folder…). Setup waits for your choice.
On a machine that’s already syncing, it doesn’t interrupt your work: it raises the same choice once, gently, showing which folder you’re currently on (“You are currently syncing … Keep it, or switch to another folder.”) so you can Keep the current folder or switch to another.

Once you’ve chosen, that choice is remembered as this machine’s Claude folder setting, so you’re never asked again. If instead only one folder holds real configuration, there’s nothing to ask: Claude Sync uses it and follows the resolution order above without a prompt.

What always stays in your home

Two things follow your home folder and do not move together with the configuration folder:

~/.claude.json always stays in your home: Claude Code does not move it under CLAUDE_CONFIG_DIR, and Claude Sync never syncs it.
The memory database ~/.claude-mem also follows your home, not the configuration folder.

Inside the Claude folder itself, Claude Sync keeps a small .knm-sync working area for its own local bookkeeping — baselines, safety backups, and locks. It is strictly local to this machine and is never synced: it never travels to your repository or to your other machines.

Several windows or sessions at once

If you open several VS Code windows or several Claude Code sessions on the same folder, you’re safe: they take turns, so your changes are never lost or duplicated. A single window drives the automatic sync; the others follow passively. If you start a manual sync while another is running, you’ll see “Another window is syncing right now — try again shortly.”

Different Claude folders, on the other hand, sync fully independently of each other.