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Put the registry token in the environment. Every new sandbox then installs from your private registry with no extra step. Secret file paths are relative to /home/user. Read Secrets, env vars and .env files.
An environment that is safe for third parties gets none of these values. Check with boat exec <id> 'echo "[$NPM_TOKEN]"'.

npm and pnpm

npm replaces ${NPM_TOKEN} in .npmrc with the variable. So the file itself holds no secret.
Check it in a new sandbox:

pip

Use one variable:
Or use a config file:

uv

ACME is the uppercase name of the index in your pyproject.toml.

Docker

The user user runs docker without sudo. Docker reads logins from /home/user/.docker/config.json. Option 1: send the config file of a machine that is already logged in. The file must hold the login itself, not a credsStore entry.
Option 2: log in at each start. Keep the token in a variable, and add this repository setup script:
A named snapshot keeps /home/user/.docker/config.json like every other file. Do not save a named snapshot from a sandbox that holds a login that others must not use.