Settings UI writes IDENTITY.md and SOUL.md to root instead of agents/main/ workspace

[lijunle-bot]

Bug

When updating the main agent identity or soul via the Settings UI, the files are written to data_dir/IDENTITY.md and data_dir/SOUL.md (root) instead of data_dir/agents/main/IDENTITY.md and data_dir/agents/main/SOUL.md.

However, both load_identity_for_agent("main") and load_soul_for_agent("main") check agents/main/ first and only fall back to root. So if the agent-level files already exist, the settings updates are silently ignored at runtime.

Root Cause

IDENTITY.md

The call chain for the main agent identity update:

1. Settings UI (identity-utils.js) calls updateIdentity(fields, { agentId: "main" })
2. This sends RPC agents.identity.update with agent_id: "main"
3. If that fails (method not found fallback), it sends agent.identity.update without agent_id
4. agent.identity.update handler (services.rs:322-330): for main agent, delegates to onboarding.identity_update()
5. onboarding.identity_update() (service.rs:271): calls moltis_config::save_identity(&identity) — writes to root data_dir/IDENTITY.md

But load_identity_for_agent("main") (loader.rs:374-380) reads from agents/main/IDENTITY.md first and only falls back to root:

pub fn load_identity_for_agent(agent_id: &str) -> Option<AgentIdentity> {
    if agent_id == "main" {
        let main_path = agent_workspace_dir("main").join("IDENTITY.md");
        if let Some(identity) = load_identity_from_path(&main_path) {
            return Some(identity);
        }
        return load_identity();  // fallback to root
    }
    // ...
}

SOUL.md (same pattern)

The save path for soul updates:

1. Settings UI calls agent.identity.update_soul
2. identity_update_soul() (service.rs:295): calls moltis_config::save_soul() — writes to root data_dir/SOUL.md

But load_soul_for_agent("main") (loader.rs:515-523) reads from agents/main/SOUL.md first:

pub fn load_soul_for_agent(agent_id: &str) -> Option<String> {
    if agent_id == "main" {
        let main_path = agent_workspace_dir("main").join("SOUL.md");
        if let Some(soul) = load_workspace_markdown(main_path) {
            return Some(soul);
        }
        return load_soul();  // fallback to root
    }
    // ...
}

Meanwhile, save_soul() writes to soul_path() which is data_dir()/SOUL.md (root).

Consequence

• Both root IDENTITY.md and SOUL.md should not be primary write targets for the main agent
• If agents/main/ versions exist, any changes through onboarding or the settings page are invisible
• The UI string "Saved to IDENTITY.md in your workspace root" is misleading

Suggested Fix

IDENTITY.md

In crates/onboarding/src/service.rs, both at line 110 and line 271, replace:

moltis_config::save_identity(&ws.identity)

with:

moltis_config::save_identity_for_agent("main", &ws.identity)

SOUL.md

In crates/onboarding/src/service.rs line 295, the identity_update_soul() method should call a new save_soul_for_agent("main", soul) function (analogous to save_identity_for_agent) that writes to agents/main/SOUL.md instead of root.

Alternatively, save_soul() could be updated to always write to the agent workspace when the agent_id is known.

The root files can remain as legacy fallbacks for installations that do not yet have agents/main/ versions.

Steps to Reproduce

1. Ensure data_dir/agents/main/IDENTITY.md and data_dir/agents/main/SOUL.md exist
2. Edit agent name or soul text via Settings UI
3. Observe root-level files are updated, but agent-level files are unchanged
4. Runtime continues using the old agent-level files