Fix app-server agent storage paths

[Bortlesboat]

Summary

• Store app-server project agents under .cortex/agents and user agents under the OS config-dir cortex/agents path.
• Use one set of path helpers across list/get/create/update/delete/import.
• Add regression coverage for project agent create/list discovery via the standard directory.

Tests

• cargo test -p cortex-app-server project_agent -- --nocapture
• cargo test -p cortex-app-server api::agents -- --nocapture
• cargo test -p cortex-app-server --lib -- --skip tools::shell::tests::test_execute_shell
• cargo check -p cortex-app-server
• cargo fmt --check --package cortex-app-server
• git diff --check

Note: full cargo test -p cortex-app-server currently has an unrelated Windows failure in tools::shell::tests::test_execute_shell because echo is a shell built-in rather than a standalone executable.

[greptile-apps]

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