docs: add Linux CLI terminal installation instructions and clean up outdated steps

[xrissoula]

Description

This PR updates the Polykey CLI installation documentation to:

• Clean up and streamline the Linux installation steps
• Clarify terminal behavior when running the polykey agent start command
• Add onboarding guidance for users interacting with the agent via terminal

This resolves confusion around why subsequent Polykey commands don’t work in the same terminal window after starting the agent, addressing a critical usability gap in the existing CLI documentation.

Issues Fixed

• Fixes Improve CLI and docs to guide users on agent terminal behavior #144

Tasks

• 1. Remove duplicated and outdated Linux installation instructions
• 2. Clearly document that the agent takes over the terminal window
• 3. Instruct users to open a new terminal window to issue further commands (e.g., vault creation)
• 4. Mention the need to restart the agent if terminated or after reboot
• 5. more to follow, after receiving feedback from @CMCDragonkai @aryanjassal @faithveloro09

Final checklist

• Domain specific tests
• Full tests
• Updated inline-comment documentation
• Lint fixed
• Squash and rebased
• Sanity check the final build

[xrissoula]

The PR is failing due to a lint.mjs shellcheck step that uses find -regextype, which isn’t supported on macOS or the default GitHub runner. No .sh files were added or changed in this PR, so this isn’t related to the actual changes. @CMCDragonkai @aryanjassal

[aryanjassal]

I guess a platform-agnostic way to do this could be this? I'll have to dig into this later.

find ./src ./scripts -type f | grep -E '\\.sh$' | xargs shellcheck

[aryanjassal]

Actually nevermind, that is not the issue. We use nix wrappers in the CI so that wouldn't be an issue. If we look at the error, this is buried between the error somewhere.

Checking formatting...
[warn] docs/Getting-Started/polykey-cli/installation.md
[warn] Code style issues found in the above file. Run Prettier with --write to fix.

It says that prettier found some code issues so you gotta fix that instead. Try running npm run lintfix to update all the files. If any changes are observed, then the lint was catching an issue correctly.

[aryanjassal]

It's mostly good, just a minor update