Docs: clarify CLI terminal usage and streamline Linux installation 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 Remove duplicated and outdated Linux installation instructions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]

closing and remaking this PR because I created it off of the wrong branch. it is now PR #144