fix(cli): prefer .kilo config directory

[marius-kilocode]

Repositories can retain configuration in .opencode and .kilocode while adopting the canonical .kilo directory. The previous discovery order allowed .opencode entries to override .kilo, producing unexpected config, command, agent, and overlay values.

Load compatibility directories first and .kilo last so the canonical Kilo configuration has the highest precedence while preserving legacy fallback behavior. Config source reporting and linked-worktree fallback ordering now follow the same precedence.

[kilo-code-bot]

Code Review Summary

Status: 1 Issue Found | Recommendation: Address before merge

Overview

Severity	Count
CRITICAL	0
WARNING	1
SUGGESTION	0

Fix these issues in Kilo Cloud

Issue Details (click to expand)

WARNING

File	Line	Issue
packages/opencode/src/config/paths.ts	29	Removing .opencode from config-directory discovery drops legacy directory-based config entirely, including the TUI migration path that would otherwise preserve theme and keybinds on upgrade.

Files Reviewed (42 files)

• .changeset/prefer-kilo-config.md - 0 issues
• packages/kilo-docs/pages/automate/extending/plugins.md - 0 issues
• packages/kilo-docs/pages/code-with-ai/platforms/cli.md - 0 issues
• packages/kilo-docs/pages/contributing/architecture/cli-runtime.md - 0 issues
• packages/kilo-docs/pages/customize/custom-modes.md - 0 issues
• packages/opencode/specs/tui-plugins.md - 0 issues
• packages/opencode/src/cli/cmd/mcp.ts - 0 issues
• packages/opencode/src/cli/cmd/tui/config/tui.ts - 0 issues
• packages/opencode/src/cli/cmd/tui/context/theme.tsx - 0 issues
• packages/opencode/src/cli/cmd/tui/feature-plugins/home/tips-view.tsx - 0 issues
• packages/opencode/src/cli/cmd/tui/plugin/runtime.ts - 0 issues
• packages/opencode/src/config/config.ts - 0 issues
• packages/opencode/src/config/paths.ts - 1 issue
• packages/opencode/src/file/ripgrep.ts - 0 issues
• packages/opencode/src/kilocode/config/config.ts - 0 issues
• packages/opencode/src/kilocode/config/overlay.ts - 0 issues
• packages/opencode/src/kilocode/config/sources.ts - 0 issues
• packages/opencode/src/kilocode/docs/migration.md - 0 issues
• packages/opencode/src/kilocode/docs/rules-migration.md - 0 issues
• packages/opencode/src/kilocode/permission/config-paths.ts - 0 issues
• packages/opencode/src/kilocode/skills/kilo-config.md - 0 issues
• packages/opencode/src/kilocode/tui/config.ts - 0 issues
• packages/opencode/src/plugin/install.ts - 0 issues
• packages/opencode/test/agent/agent.test.ts - 0 issues
• packages/opencode/test/cli/tui/plugin-loader.test.ts - 0 issues
• packages/opencode/test/config/config.test.ts - 0 issues
• packages/opencode/test/config/tui.test.ts - 0 issues
• packages/opencode/test/kilocode/config/config.test.ts - 0 issues
• packages/opencode/test/kilocode/plugin-dependencies.ts - 0 issues
• packages/opencode/test/kilocode/server/config-overlay.test.ts - 0 issues
• packages/opencode/test/kilocode/server/config-sources.test.ts - 0 issues
• packages/opencode/test/kilocode/server/httpapi-exercise-scenarios.ts - 0 issues
• packages/opencode/test/kilocode/server/tui-config.test.ts - 0 issues
• packages/opencode/test/plugin/auth-override.test.ts - 0 issues
• packages/opencode/test/plugin/install-concurrency.test.ts - 0 issues
• packages/opencode/test/plugin/install.test.ts - 0 issues
• packages/opencode/test/provider/provider.test.ts - 0 issues
• packages/opencode/test/server/httpapi-provider.test.ts - 0 issues
• packages/opencode/test/server/httpapi-sdk.test.ts - 0 issues
• packages/opencode/test/skill/skill.test.ts - 0 issues
• packages/opencode/test/tool/registry.test.ts - 0 issues
• packages/opencode/test/tool/skill.test.ts - 0 issues

Previous Review Summary (commit 117a0d6)

Current summary above is authoritative. Previous snapshots are kept for context only.

Previous review (commit 117a0d6)

Status: No Issues Found | Recommendation: Merge

Files Reviewed (8 files)

• .changeset/prefer-kilo-config.md
• packages/opencode/src/config/config.ts
• packages/opencode/src/config/paths.ts
• packages/opencode/src/kilocode/config/overlay.ts
• packages/opencode/src/kilocode/config/sources.ts
• packages/opencode/test/kilocode/config/config.test.ts
• packages/opencode/test/kilocode/server/config-overlay.test.ts
• packages/opencode/test/kilocode/server/config-sources.test.ts

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_{Reviewed by gpt-5.4-20260305 · Input: 167.2K · Output: 23.3K · Cached: 2.9M}

_{Review guidance: REVIEW.md from base branch main}