Fixes #3148

Problem

The migrate_legacy_knowledge_base function was incorrectly moving other agent directories into the current agent's directory when running /knowledge show. This created nested directory structures like:

~/.aws/amazonq/knowledge_bases/
  agent_a/
    agent_b/  <-- Wrong! Agent B nested inside Agent A

Root Cause

The migration logic didn't distinguish between files and directories when filtering entries in the knowledge_bases root. It was treating other agent directories as "legacy files" to migrate.

Solution

Added a check to ensure only FILES are migrated from the root directory, leaving other agent directories untouched.

Testing

• Verified the filter now checks path.is_file() before migrating
• Other agent directories will no longer be moved into the current agent's directory