fix(agents): write custom agents to loader paths

[OnlyYu1996]

Fixes PlatformNetwork/bounty-challenge#53529.
Fixes PlatformNetwork/bounty-challenge#53528.

Summary

• Make the engine CreateAgent tool write standard Markdown custom-agent files under .cortex/agents instead of orphaned TOML files.
• Make app-server agent create/import write to .cortex/agents / ~/.cortex/agents, matching the standard loader paths.
• Keep .factory/agents as a legacy read/update/delete fallback so existing app-server-created agents are still discoverable.
• Add regression coverage for standard app-server paths, Markdown parsing, and engine-created files loading through the standard custom-agent loader.

Validation

• cargo +1.90.0 fmt --package cortex-engine --package cortex-app-server --check
• git diff --check

Targeted cargo +1.90.0 test -p cortex-engine test_create_agent_project_location -- --nocapture is blocked in this Windows/MSVC environment before crate tests run by the existing aws-lc-sys C build failure.

[greptile-apps]

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