[Bug] Remove legacy agents directory during setup/update to prevent duplicate installed skills

[Yeachan-Heo]

Summary

When OmX runs setup/update, it should detect legacy agents/ install locations and remove or migrate them automatically. Right now old legacy agent directories can survive alongside the current layout, which causes duplicated installed skills/agents to appear.

Problem

Legacy agents directories from older installs are not being cleaned up during setup/update.
Because of that, skill/agent content can be loaded from both the legacy location and the current location, producing duplicate installed entries.

Expected behavior

• setup/update detects legacy agents/ directories
• legacy directories are either safely removed or migrated
• resulting install state contains only the canonical/current location
• duplicate installed skills/agents do not appear after upgrade

Actual behavior

• legacy directory can remain after setup/update
• duplicate installed skills/agents appear in the resulting environment

Proposed direction

• add legacy install-path detection during setup/update
• remove legacy agents/ tree when it is clearly superseded by the canonical layout
• if destructive removal needs guardrails, log exactly what was removed and/or back it up first
• add regression coverage for upgrade-from-legacy layout

Why this matters

Broken/duplicate skill state makes OmX look unreliable during upgrades and creates confusing runtime behavior.

[Jah-yee]

This duplicate agents issue could be solved by adding a migration step that checks for the legacy directory existence before creating the new one, with appropriate cleanup. Happy to open a PR for this if you approve!