effect: move tool flags into RuntimeFlags

[kitlangton]

Summary

• Adds tool-selection runtime flags to RuntimeFlags using ConfigService definitions.
• Migrates ToolRegistry tool visibility decisions from direct Flag reads to RuntimeFlags.
• Migrates WebSearchTool provider selection to use the same RuntimeFlags values as registry visibility.
• Updates tool registry tests to use explicit RuntimeFlags.layer(...) variants instead of mutating Flag.OPENCODE_EXPERIMENTAL_SCOUT.
• Provides explicit default RuntimeFlags.layer() in open ToolRegistry.layer test compositions.

Notes

• I started on OPENCODE_EXPERIMENTAL_WORKSPACES first, but it is too coupled to legacy mutable Flag and closed default layers for a small safe PR. This tool-registry cluster is a smaller step that proves the pattern.
• No compatibility bridge was added: tests that need different runtime flags now choose a different layer.

Verification

• bun run test -- test/effect/runtime-flags.test.ts test/tool/registry.test.ts test/tool/websearch.test.ts test/session/snapshot-tool-race.test.ts
• bunx prettier --check packages/opencode/src/effect/runtime-flags.ts packages/opencode/src/tool/registry.ts packages/opencode/src/tool/websearch.ts packages/opencode/test/effect/runtime-flags.test.ts packages/opencode/test/tool/registry.test.ts packages/opencode/test/session/snapshot-tool-race.test.ts packages/opencode/test/session/prompt.test.ts
• git diff --check

Simplify review

• Removed the mutable Flag compatibility bridge.
• Switched scout tests to explicit layer variants.
• Reused the local bool(...) helper for all false-default boolean flags.
• Fixed websearch execution to use the same runtime flags as registry visibility.

Typecheck

bun typecheck currently fails on unrelated provider/tool metadata type issues already present in this worktree dependency state; focused tests pass.