fix(config): prevent config wipeout on resolution or validation failure

[mukhtharcm]

Description

This PR ensures the configuration is preserved when config.apply is used, even if the current config has resolution errors (missing env vars or broken includes).

Why it was needed

A regression was introduced in a36735b (Env Var Substitution) where a resolution failure would return an empty object {}. When tools like model switching (config.apply) then merged their changes into this empty object and wrote it back, the user's entire config was wiped out.

Changes

1. Robust Loader (src/config/io.ts): Failure during $include resolution or ${VAR} substitution now returns the best-effort config instead of {}. This ensures we don't "forget" the existing data.
2. Safe Merging (src/gateway/server-methods/config.ts): Updated config.apply to use applyMergePatch against the snapshot, providing a second layer of protection against destructive overwrites during quick toggles/swaps.

Notes

This extends the logic from PR #764 to cover new failure modes introduced by recent config features.

[steipete]

Config semantics today:

• config.set + config.apply = full replace (user intent: “here’s the whole
  config”).
• config.patch = merge‑patch (partial updates; null deletes).

PR change made config.apply behave like merge‑patch:

• Missing keys no longer delete → stale config sticks around (surprising for
  “apply”).
• If base config is invalid, merge drags invalid keys forward → validation keeps
  failing.

[steipete]

Landed on main with updated config safety + backup rotation; kept latest Fixes ordering in CHANGELOG while resolving conflicts.

Commit: f8e673c