Config.update() writes runtime local config to ignored project-root config.json (re-open)

Description

Runtime local config updates made through Config.update() do not round-trip through instance disposal/reload correctly.

Config.update() writes to project-root config.json, but fresh project config loading reads the normal opencode.json / opencode.jsonc paths and local .opencode/opencode.json[c] overlays instead.

Because of that mismatch, a runtime config update can appear to work immediately, then disappear after the instance is disposed and reloaded.

Related:

• Duplicate of #28966 (auto-closed after inactivity)
• Previous fix attempt PR #28967 was closed unmerged, the bug is still present on dev

Proposed fix

Write runtime local updates to the file the loader reads last (existing .opencode/opencode.jsonc, else .opencode/opencode.json, else plain opencode.json / opencode.jsonc), merging with existing content.

Plugins

No response

OpenCode version

v1.18.2 and current dev

Steps to reproduce

1. Start with a project where a runtime config update changes agent config through the config update path
2. Trigger the config update
3. Let the instance get disposed/reloaded
4. Use the updated config again after reload

Screenshot and/or share link

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Operating System

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Terminal

No response