Consolidate config files into a single directory (~/.deepseek/)

[douglarek]

Problem

DeepSeek TUI currently splits its persistent configuration across two separate directory trees:

File	Path	Purpose
config.toml	~/.deepseek/config.toml	API keys, providers, network policy, hooks, LSP, skills installer, snapshots, etc.
settings.toml	~/.config/deepseek/settings.toml	UI/behavior preferences (auto_compact, locale, composer density, sidebar width, etc.)
tui.toml	~/.deepseek/tui.toml	TUI appearance (theme, font_size, keybinds) — reserved, not yet wired (#657)

EN: This dual-directory split is confusing for users and has no technical justification. A user who edits ~/.deepseek/config.toml following deepseek doctor's instructions later discovers that /config --save writes to a completely different directory they didn't know existed. The slash-command write targets are also internally inconsistent: /config --save writes to settings.toml (under ~/.config/deepseek/), but /statusline writes to config.toml (under ~/.deepseek/), and /config mcp_config_path --save also writes to config.toml — three different targets for what the user sees as "the config command."

CN: 双目录配置拆分让用户非常困惑，而且没有任何技术必要性。用户按照 deepseek doctor 的提示编辑了 ~/.deepseek/config.toml，之后却发现 /config --save 写入了一个完全不同的、他们根本不知道其存在的目录。slash 命令的写入目标也内部不一致：/config --save 写入 settings.toml（在 ~/.config/deepseek/ 下），但 /statusline 写入 config.toml（在 ~/.deepseek/ 下），/config mcp_config_path --save 也写入 config.toml——用户眼中的"配置命令"实际上有三个不同的写入目标。

Additionally, there is content overlap: model/default_model appears in both config.toml and settings.toml. The TuiPrefs struct (tui.toml) overlaps with Settings (settings.toml) — both store TUI-related knobs. And ~/.deepseek/ is a misnomer: it's not a config directory but an application data directory that mixes user-editable config files with auto-generated runtime artifacts (sessions, audit logs, caches, stashes, embeddings), making it impossible for users to tell what's safe to edit.

此外，还有内容重叠问题：model/default_model 同时存在于 config.toml 和 settings.toml 中。TuiPrefs（tui.toml）和 Settings（settings.toml）都存储 TUI 相关设置，功能重叠。而且 ~/.deepseek/ 名称有误导性——它不是一个单纯的配置目录，而是一个应用程序数据目录，混杂了用户可编辑的配置文件（config.toml、tui.toml、mcp.json、execpolicy.toml、notes.txt、memory.md）和运行时自动生成的产物（sessions/、audit.log、cache/、secrets/、tool_outputs/、embeddings/ 等），用户完全无法区分哪些可以手动修改、哪些不能碰。

An outdated comment in crates/tui/src/tui/model_picker.rs:12 still references ~/.deepseek/settings.toml, which is no longer the production path — this has been stale since the settings path moved to dirs::config_dir().

crates/tui/src/tui/model_picker.rs:12 的注释仍然引用 ~/.deepseek/settings.toml，而这个路径已经不是生产环境中的实际路径——自 settings 路径迁移到 dirs::config_dir() 后该注释就已经过时。

Proposed solution

EN: Consolidate all user-editable config files under ~/.deepseek/:

• Move settings.toml from ~/.config/deepseek/settings.toml to ~/.deepseek/settings.toml (with a migration step that copies from the old location on first launch).
• Unify /config --save and /statusline to write to the same files in the same directory.
• Clearly separate user-editable config files from auto-generated runtime artifacts, either through a config/ subdirectory or explicit documentation.

CN: 将所有用户可编辑的配置文件统合到 ~/.deepseek/ 下：

• 将 settings.toml 从 ~/.config/deepseek/settings.toml 迁移到 ~/.deepseek/settings.toml（首次启动时自动从旧路径复制）。
• 统合 /config --save 和 /statusline 的写入目标，使它们写入同一目录下的同一个文件集。
• 清晰地区分用户可编辑的配置文件与自动生成的运行时数据，可以通过 config/ 子目录或明确文档来实现。

Classification of files in ~/.deepseek/

EN — User-editable config files (documented, safe to edit):

File	Edited by
config.toml	Manual editing, deepseek auth set, deepseek skill install, /statusline (via persist_status_items), /config mcp_config_path --save
tui.toml	Manual editing (reserved, not yet wired — #657)
mcp.json	Manual editing, deepseek mcp add-self
execpolicy.toml	Manual editing
notes.txt	Manual editing (or # quick-add in composer)
memory.md	Manual editing (or # quick-add in composer, when [memory] enabled = true)

Auto-generated runtime files (do not edit):

File	Written by
settings.toml	/config --save (Settings)
audit.log	Network auditor, credential events, tool approvals
events.jsonl	Hook event sink
sessions/	Session manager (saves + checkpoints + cycle archives)
tasks/runtime/events/	Runtime thread event streams
cache/skills/	Skill installer cache
embeddings/	Archive embedding cache
secrets/secrets.json	OS keyring fallback store
composer_stash.jsonl	Composer draft stash
composer_history.txt	Composer input history
tool_outputs/	Spilled large tool outputs
file-frecency.jsonl	File frecency tracker
skills_state.toml	Skill state tracker
mcp_server.toml	MCP server self-config
managed_config.toml	Managed config
requirements.toml	Requirements
workspace-trust.json	/trust add persistence
.onboarded	Onboarding marker

CN — 用户可编辑的配置文件（有文档，可以安全编辑）：

文件	修改方式
config.toml	手动编辑、deepseek auth set、deepseek skill install、/statusline（通过 persist_status_items）、/config mcp_config_path --save
tui.toml	手动编辑（预留，尚未接线 — #657）
mcp.json	手动编辑、deepseek mcp add-self
execpolicy.toml	手动编辑
notes.txt	手动编辑（或在输入框中用 # 快速追加）
memory.md	手动编辑（或在输入框中用 # 快速追加，需要 [memory] enabled = true）

自动生成的运行时文件（不要编辑）：

文件	写入来源
settings.toml	/config --save（Settings）
audit.log	网络审计器、凭证事件、工具审批
events.jsonl	Hook 事件 sink
sessions/	会话管理器（保存 + 检查点 + 循环归档）
tasks/runtime/events/	运行时线程事件流
cache/skills/	技能安装器缓存
embeddings/	归档嵌入缓存
secrets/secrets.json	OS keyring 降级存储
composer_stash.jsonl	输入框草稿暂存
composer_history.txt	输入框历史
tool_outputs/	溢出的大型工具输出
file-frecency.jsonl	文件使用频率追踪
skills_state.toml	技能状态追踪
mcp_server.toml	MCP 服务器自配置
managed_config.toml	托管配置
requirements.toml	需求文件
workspace-trust.json	/trust add 持久化
.onboarded	新手引导标记

Alternatives considered

EN:

1. Move everything to ~/.config/deepseek/ (XDG-compliant). Rejected because ~/.deepseek/ already contains >20 auto-generated runtime artifacts (sessions, caches, audit logs, stashes) that are not "config" per XDG. Moving the entire state tree to ~/.config/ would violate XDG spirit worse than the current split. And ~/.deepseek/config.toml is already well-known to existing users.
2. Keep the split but add symlinks. Adds fragility and platform-specific edge cases (Windows symlink permissions, snap/Flatpak sandbox restrictions).
3. Merge config.toml and settings.toml into one file. Reduces confusion about "which file has what" but doesn't address the directory split itself; also risks bloating a single file with heterogeneous concerns and makes safe round-trip writes harder (programmatic updates to one section could clobber unrelated manual edits).

CN:

1. 全部迁移到 ~/.config/deepseek/（XDG 兼容）。否决，因为 ~/.deepseek/ 已经包含超过 20 个自动生成的运行时产物（sessions、caches、audit logs、stashes），这些按 XDG 规范不属于 "config"。将整个状态树迁移到 ~/.config/ 会比当前分裂更违背 XDG 精神。且 ~/.deepseek/config.toml 已经是现有用户熟知的路径。
2. 保持分裂但添加软链接。 增加脆弱性和平台特化边界情况（Windows 软链接权限、snap/Flatpak 沙箱限制）。
3. 合并 config.toml 和 settings.toml 为一个文件。 减少"哪个文件有什么"的困惑，但不解决目录分裂本身的问题；还会让单个文件膨胀、混合异质关注点，并使安全的 round-trip 写入更困难（对某一节的程序化更新可能破坏不相关的手动编辑）。

Additional context

• /config approval_mode and /config model (without --save) modify App state in-memory only and are intentionally session-scoped. This is reasonable behavior but should be documented alongside the persistence distinction.
• DEEPSEEK_CONFIG_PATH currently redirects the parent directory for both config.toml and settings.toml — after consolidation this would simply point at the ~/.deepseek/ alternative root.
• The TuiPrefs struct at ~/.deepseek/tui.toml (#657) should be either fully wired or removed before consolidation, so the final file layout is stable.

[Hmbown]

thank you so much. great ideas.

[Hmbown]

Investigated for v0.8.48. Config is currently split across three directories:

• ~/.deepseek/ — config.toml, tui.toml, mcp_server.toml, runtime state (primary)
• ~/.codewhale/ — partially-migrated copy from v0.8.44 (incomplete migration)
• ~/.config/deepseek/ — settings.toml for UI preferences (XDG path, outlier)

The migration to ~/.codewhale/ is partial and incomplete. settings.toml is the only file still using the XDG config directory.

Plan:

1. Add settings.toml resolution to ~/.deepseek/settings.toml with XDG fallback
2. Update Settings::path() to prefer ~/.deepseek/settings.toml
3. On first load, migrate existing ~/.config/deepseek/settings.toml → ~/.deepseek/
4. Add a deprecation notice for ~/.codewhale/ pointing users to ~/.deepseek/
5. Update doctor and docs to reference the single canonical location

This can be done incrementally — step 1 alone would solve the immediate confusion without breaking existing installs.