Summary

The /verbose (and Ctrl+O) toggle previously reset to off on every CLI
launch because the in-memory showReasoning bool was never written
back to the config. This adds an optional ui.show_thinking field
(default false, fully backward-compatible) and persists every flip
off the bubbletea event loop so the next session opens with the
reasoning block in the same state.

Fixes #3312.

Changes

• internal/config/config.go — new UIConfig.ShowThinking bool with toml:"show_thinking", defaults to false.
• internal/config/render.go — RenderTOMLForScope emits show_thinking = true only when set, with a commented-out placeholder only in RenderScopeFull so unmodified project configs stay byte-identical.
• internal/cli/cli.go — chatREPL now calls a new m.applyConfig(cfg) helper.
• internal/cli/chat_tui.go —
  • new applyConfig(cfg) method: seeds the TUI from a loaded config, using OR semantics so a persisted ShowThinking=true does not stomp the Termux native-scrollback default.
  • toggleVerboseReasoning spawns a goroutine that calls persistShowThinking(show), capturing show into a local first so the save goroutine reads a stable value (no race with the Update goroutine's write to m.showReasoning).
  • new persistShowThinking(show bool) error method: writes the preference to the user-level config via SaveTo(config.UserConfigPath()).

Design notes

Why user config, not project config. show_thinking is a personal
viewing preference; writing it to a project-local reasonix.toml that
may be git-committed would leak the user's setting to every
collaborator on the repo. The same rationale as NotificationsConfig
et al. — viewing preferences belong in ~/.config/reasonix/config.toml.
Note: a project reasonix.toml with show_thinking = false will
silently win on the next load (project > user priority in Load),
which matches the long-standing merge semantics.

Why async save. The bubbletea Update() goroutine must not block
on disk I/O. SaveTo's atomic temp+rename makes racing writes safe on
disk (last-writer-wins, never a torn file); a coalescer/debouncer is
left as a possible follow-up.

Scope of the fix. Per the issue, the --show-thinking flag in
non-interactive run mode and the desktop app's reasoning toggle
(internal/serve/, desktop/) are out of scope and explicitly
unaffected. The web/desktop frontends have their own
TextSink.showReasoning field.

Tests

go test ./internal/config/  → ok
go test ./internal/cli/     → ok

New tests (all passing):

The applyConfig extraction is the testability-driven refactor that
closes the gap identified in review: previously, deleting the four
applyConfig lines would still pass every existing test. The new
TestApplyConfigRespectsShowThinking covers that regression.

Manual verification

1. Build: go build ./cmd/reasonix
2. Launch: ./reasonix chat (or reasonix.exe on Windows)
3. Type /verbose → notice "verbose on — thinking text will be shown"
4. /quit
5. Reopen: reasoning block is expanded by default
6. Inspect ~/.config/reasonix/config.toml (or %AppData%\reasonix\config.toml on Windows):

   [ui]
   show_thinking = true

7. Type /verbose again → notice "verbose off"
8. Reopen → reasoning block is collapsed, and the config now shows the field with the default value (commented placeholder in the full-render path).

Out of scope

• Debouncing rapid toggles (current behavior: 10 toggles = 10 atomic writes, all safe via temp+rename).
• Surfacing a user-visible notice when Save fails (currently slog.Warn; the in-TUI notice fires regardless of save success — matches the project's existing preference-persistence pattern, e.g. /effort).
• The web/desktop frontends' reasoning toggles.