harness: apply system_prompt_flag in ContainerScriptHarness.GetCommand

[ptone]

Problem

The system_prompt_flag field declared in harness config.yaml (e.g. --system-prompt for claude) was never applied to the CLI command. ContainerScriptHarness.GetCommand() built args without reading SystemPromptFlag or the staged system prompt file. The field existed in HarnessCommandConfig but was dead code.

The old builtin ClaudeCode struct handled this correctly — the container-script migration lost it.

Fix

In pkg/harness/container_script_harness.go:

• Added agentHome field to ContainerScriptHarness, populated during Provision()
• GetCommand() calls readSystemPrompt() after building args
• readSystemPrompt() reads from staged inputs path first (.scion/harness/inputs/system-prompt.md), falls back to native harness location for resume scenarios
• If SystemPromptFlag is set and file has content, appends [flag, content] to command args
• File-not-found and empty SystemPromptFlag are silent no-ops

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[gemini-code-assist]

Code Review

This pull request updates ContainerScriptHarness to capture agentHome during provisioning and read the system prompt from staged or native files to append to the command arguments. A critical issue was identified where agentHome might not be populated during resume scenarios because Provision() is not called, which would cause the system prompt to be silently ignored. To resolve this, it is recommended to capture agentHome in other lifecycle methods like GetEnv and HasSystemPrompt.

[gemini-code-assist]

If the agent is resumed, Provision() is typically not called on the newly instantiated ContainerScriptHarness. As a result, c.agentHome will remain empty, causing readSystemPrompt() to return early and silently ignore the system prompt. This defeats the fallback mechanism for resume scenarios.

To ensure c.agentHome is populated during resume scenarios, capture agentHome in other methods of ContainerScriptHarness that receive it, such as GetEnv and HasSystemPrompt.

For example, you can update those methods like this:

func (c *ContainerScriptHarness) GetEnv(agentName, agentHome, unixUsername string) map[string]string {
	c.agentHome = agentHome
	// ... existing code ...
}

func (c *ContainerScriptHarness) HasSystemPrompt(agentHome string) bool {
	c.agentHome = agentHome
	// ... existing code ...
}