Improve kernel supervisor wrapper to make environment more predictable and configurable

[jmcphers]

This change updates the kernel supervisor to 0.1.40, which, together with the Positron changes in this PR, addresses a number of related issues around the supervisor's lifecycle and environment.

The changes are as follows:

• The supervisor is itself run in a login shell, and it can start kernels in login shells too, so that each kernel start (or restart) runs login scripts and picks up changes to e.g. .bash_profile. This behavior does have a minor impact on startup time, so I've made it optional.
• The supervisor wrapper script now invokes nohup instead of the other way around. This inversion allows us to better control the behavior of nohup and prevent it from littering the project with nohup.out files.
• The supervisor can now adjust its shutdown timeout on the fly. This allows the shutdown timeout setting to work correctly in the Remote SSH environment, and also makes this setting take effect immediately instead of requiring a restart.
• The supervisor is now smarter about environment variables on Windows, addressing an issue that caused PATH to (non deterministically) be incorrect in R and Python sessions.

Addresses #6757
Addresses #7215
Addresses #7274
Addresses #7537

Release Notes

New Features

• Shell login scripts (e.g. .bash_profile, .zprofile) are now run when starting Python and R sessions (Supervisor: Run kernels in a login shell, or otherwise run startup scripts #6757)

Bug Fixes

• Fixed nohup.out file littering projects when kernel supervisor is set to run after Positron exits (File nohup.out generated by Positron Supervisor #7215)
• Shutdown idle timeout now respected in Remote SSH sessions (Supervisor: Shutdown Timeout not respected for Remote SSH #7537)
• On Windows, user and system environment variables now appear correctly inside R and Python sessions ([Bug] Positron console fails to inherit PATH "User Variables" on Windows #7274)

QA Notes

Note that the supervisor and kernels are run in login shells, not interactive shells. This means that variables from .bashrc may not be visible; use e.g. .bash_profile instead. The system will attempt to use your default shell, which is zsh on recent macOS, so make sure you edit the profile script that matches your $SHELL.

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[Copilot]

Pull Request Overview

This PR upgrades the kernel supervisor to v0.1.40 and makes its environment and lifecycle more configurable and predictable.

• Introduces a runInShell flag to optionally start supervisor and kernels in login shells
• Refactors the wrapper script to invoke nohup internally and avoid stray nohup.out files
• Adds API endpoints to get/set server configuration (e.g. idle shutdown hours) and dynamic timeout updates

Reviewed Changes

Copilot reviewed 11 out of 11 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
extensions/positron-supervisor/src/kcclient/model/serverStatus.ts	Add version and processId fields to the server status model
extensions/positron-supervisor/src/kcclient/model/serverConfiguration.ts	Introduce the ServerConfiguration model
extensions/positron-supervisor/src/kcclient/model/newSession.ts	Add runInShell flag to session creation
extensions/positron-supervisor/src/kcclient/model/models.ts & .openapi-generator/FILES	Export the new configuration model
extensions/positron-supervisor/src/kcclient/api/defaultApi.ts	Add getServerConfiguration and setServerConfiguration methods
extensions/positron-supervisor/src/KallichoreSession.ts	Pass runInShell from settings into new sessions
extensions/positron-supervisor/src/KallichoreAdapterApi.ts	Hook config changes for idle shutdown, refactor nohup logic, track real PID
extensions/positron-supervisor/resources/supervisor-wrapper.sh	Support optional nohup, run in login shell, and cleaned redirection
extensions/positron-supervisor/package.json & package.nls.json	Add kernelSupervisor.runInShell setting and bump kallichore version

Comments suppressed due to low confidence (1)

extensions/positron-supervisor/src/kcclient/api/defaultApi.ts:452

• New methods getServerConfiguration and setServerConfiguration are added but there are no corresponding unit or integration tests. Adding tests will ensure these endpoints work as expected.

public async getServerConfiguration (options: {headers: {[name: string]: string}} = {headers: {}}) : Promise<{ response: http.IncomingMessage; body: ServerConfiguration;  }> {