docs: clarify where secrets can be templated from (#11865)

* docs: clarify where secrets are resolved from and IDE vs CLI differences

Reorganizes the secrets FAQ to lead with how to use secrets, then clearly
lists the resolution order. Adds a warning that IDE extensions cannot read
shell environment variables — the most common source of confusion.

Fixes #9081

* Use Mintlify <Warning> component instead of :::warning syntax

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Co-authored-by: continue[bot] <230936708+continue[bot]@users.noreply.github.com>