fix: clear profile endpoint overrides

[albert20260301]

Summary

• remove stored profile endpoint override keys instead of rewriting them as empty values
• keep later stored endpoint values visible to config lookup, including tests that append profile config entries

Verification

• bun test tests/configure.test.ts tests/management.test.ts
• bun test "$PWD"/tests/*.test.ts

Stacked on #46 to repair the failing Test CLI job.