feat(coding-agent): persist system and append prompts to the session file

[scutifer]

This is a redo of #335

If a session is started with --system-prompt ".." or with --append-system-prompt "..", the resolved prompts are stored into the session file.

When this session is resumed later, the stored prompts are used.

If the session is resumed with a different --system-prompt or --append-system-prompt, the new ones are appended to the session file and override the older ones.

System Prompt Construction
The system prompt is constructed from 6 parts

[main prompt] + [append] + [AGENTS.md/CLAUDE.md] + [skills] + [datetime] + [cwd]
       ^              ^              ^                  ^          ^          ^
     part 1        part 2         part 3             part 4     part 5     part 6
     static        static        dynamic            dynamic    dynamic    dynamic

The session entries override parts 1 and 2. Parts 3~6 are constructed at runtime to use any new context, skills etc.

Changelog

• Added getTools() method to the Agent class for retrieving active tools.
• Updated AgentSession to restore system prompts from session context.
• Enhanced createAgentSession to support appending prompts and saving system prompts.
• Introduced new session manager entries for user-defined system prompts and appends.

[badlogic]

Looking good! Rolled this into #892, need to integrate this manually in the great refactor.