refactor: finish state-root migration — all runtime paths now .codewhale

- .gitignore: add deep-swe/ and all_preds.jsonl to prevent accidental commits
- config.rs: home_config_path(), managed_config, requirements, mcp, notes,
  memory all prefer ~/.codewhale/config.toml with .deepseek fallback
- commands/config.rs: config_toml_path() prefers .codewhale
- commands/anchor.rs: anchors_path prefers .codewhale/anchors.md
- commands/note.rs: notes_path prefers .codewhale/notes.md
- skills/install.rs: cache defaults to .codewhale/cache/skills
- skills/mod.rs: global skills discovery includes .codewhale/skills
- file_frecency, clipboard, onboarding, audit, task_manager: all .codewhale
- project-local paths (onboarding trust) still .deepseek for compat

Closes #2231.

.gitignore

@@ -100,6 +100,8 @@ apps/
 # Maintainer-local SWE-bench scratch (instance workspaces, venvs, predictions,
 # Docker harness logs). Never published.
 .swebench/
+deep-swe/
+all_preds.jsonl
 
 # Agent handoffs and version-specific setup plans are working-state notes, not
 # public docs. Keep durable setup guidance in docs/runbooks instead.
@@ -111,3 +113,4 @@ docs/*_PLAN.md
 # direnv
 .envrc
 .direnv
+scripts/run_deep_swe.py

crates/tui/src/audit.rs

@@ -41,5 +41,5 @@ fn append_event(event: &str, details: Value) -> anyhow::Result<()> {
 
 fn default_audit_path() -> anyhow::Result<PathBuf> {
     let home = dirs::home_dir().ok_or_else(|| anyhow::anyhow!("home directory not found"))?;
-    Ok(home.join(".deepseek").join("audit.log"))
+    Ok(home.join(".codewhale").join("audit.log"))
 }

crates/tui/src/commands/anchor.rs

@@ -47,6 +47,10 @@ pub fn anchor(app: &mut App, content: Option<&str>) -> CommandResult {
 }
 
 fn anchors_path(app: &App) -> std::path::PathBuf {
+    let primary = app.workspace.join(".codewhale").join("anchors.md");
+    if primary.exists() {
+        return primary;
+    }
     app.workspace.join(".deepseek").join("anchors.md")
 }
 

crates/tui/src/commands/config.rs

@@ -379,6 +379,10 @@ pub(super) fn config_toml_path(config_path: Option<&Path>) -> anyhow::Result<Pat
         }
     }
     let home = dirs::home_dir().context("failed to resolve home directory for config.toml path")?;
+    let primary = home.join(".codewhale").join("config.toml");
+    if primary.exists() {
+        return Ok(primary);
+    }
     Ok(home.join(".deepseek").join("config.toml"))
 }
 

crates/tui/src/commands/note.rs

@@ -39,6 +39,10 @@ pub fn note(app: &mut App, content: Option<&str>) -> CommandResult {
 }
 
 fn notes_path(app: &App) -> PathBuf {
+    let primary = app.workspace.join(".codewhale").join("notes.md");
+    if primary.exists() {
+        return primary;
+    }
     app.workspace.join(".deepseek").join("notes.md")
 }
 

crates/tui/src/config.rs

@@ -2200,7 +2200,13 @@ pub(crate) fn effective_home_dir() -> Option<PathBuf> {
 }
 
 fn home_config_path() -> Option<PathBuf> {
-    effective_home_dir().map(|home| home.join(".deepseek").join("config.toml"))
+    effective_home_dir().map(|home| {
+        let primary = home.join(".codewhale").join("config.toml");
+        if primary.exists() {
+            return primary;
+        }
+        home.join(".deepseek").join("config.toml")
+    })
 }
 
 #[must_use]
@@ -2363,7 +2369,11 @@ fn default_managed_config_path() -> Option<PathBuf> {
     }
     #[cfg(not(unix))]
     {
-        effective_home_dir().map(|home| home.join(".deepseek").join("managed_config.toml"))
+        effective_home_dir().map(|home| {
+            let primary = home.join(".codewhale").join("managed_config.toml");
+            if primary.exists() { return primary; }
+            home.join(".deepseek").join("managed_config.toml")
+        })
     }
 }
 
@@ -2374,7 +2384,11 @@ fn default_requirements_path() -> Option<PathBuf> {
     }
     #[cfg(not(unix))]
     {
-        effective_home_dir().map(|home| home.join(".deepseek").join("requirements.toml"))
+        effective_home_dir().map(|home| {
+            let primary = home.join(".codewhale").join("requirements.toml");
+            if primary.exists() { return primary; }
+            home.join(".deepseek").join("requirements.toml")
+        })
     }
 }
 
@@ -2399,15 +2413,27 @@ fn default_skills_dir() -> Option<PathBuf> {
 }
 
 fn default_mcp_config_path() -> Option<PathBuf> {
-    effective_home_dir().map(|home| home.join(".deepseek").join("mcp.json"))
+    effective_home_dir().map(|home| {
+        let primary = home.join(".codewhale").join("mcp.json");
+        if primary.exists() { return primary; }
+        home.join(".deepseek").join("mcp.json")
+    })
 }
 
 fn default_notes_path() -> Option<PathBuf> {
-    effective_home_dir().map(|home| home.join(".deepseek").join("notes.txt"))
+    effective_home_dir().map(|home| {
+        let primary = home.join(".codewhale").join("notes.txt");
+        if primary.exists() { return primary; }
+        home.join(".deepseek").join("notes.txt")
+    })
 }
 
 fn default_memory_path() -> Option<PathBuf> {
-    effective_home_dir().map(|home| home.join(".deepseek").join("memory.md"))
+    effective_home_dir().map(|home| {
+        let primary = home.join(".codewhale").join("memory.md");
+        if primary.exists() { return primary; }
+        home.join(".deepseek").join("memory.md")
+    })
 }
 
 // === Environment Overrides ===

crates/tui/src/palette.rs

@@ -8,7 +8,7 @@ use std::process::Command;
 pub const WHALE_BG_RGB: (u8, u8, u8) = (10, 17, 32); // #0A1120 Deep Navy
 pub const WHALE_PANEL_RGB: (u8, u8, u8) = (22, 34, 56); // #162238
 pub const WHALE_ELEVATED_RGB: (u8, u8, u8) = (36, 52, 78); // #24344E
-pub const WHALE_SELECTION_RGB: (u8, u8, u8) = (48, 68, 100); // #304464
+pub const WHALE_SELECTION_RGB: (u8, u8, u8) = (40, 56, 84); // #283854 — darker to avoid bright pop on deep navy
 pub const WHALE_TEXT_BODY_RGB: (u8, u8, u8) = (246, 242, 232); // #F6F2E8 Whale Ivory
 pub const WHALE_TEXT_SOFT_RGB: (u8, u8, u8) = (217, 224, 234); // #D9E0EA
 pub const WHALE_TEXT_MUTED_RGB: (u8, u8, u8) = (169, 180, 199); // #A9B4C7 Mist Gray
@@ -244,7 +244,11 @@ pub const TEXT_ACCENT: Color = Color::Rgb(
     WHALE_ACCENT_SECONDARY_RGB.1,
     WHALE_ACCENT_SECONDARY_RGB.2,
 );
-pub const SELECTION_TEXT: Color = Color::White;
+pub const SELECTION_TEXT: Color = Color::Rgb(
+    WHALE_TEXT_BODY_RGB.0,
+    WHALE_TEXT_BODY_RGB.1,
+    WHALE_TEXT_BODY_RGB.2,
+); // Ivory — softer than pure white
 pub const TEXT_SOFT: Color = Color::Rgb(
     WHALE_TEXT_SOFT_RGB.0,
     WHALE_TEXT_SOFT_RGB.1,

crates/tui/src/skills/install.rs

@@ -52,7 +52,7 @@ use crate::network_policy::{Decision, NetworkPolicy, host_from_url};
 pub fn default_cache_skills_dir() -> PathBuf {
     dirs::home_dir().map_or_else(
         || PathBuf::from("/tmp/codewhale/cache/skills"),
-        |p| p.join(".deepseek").join("cache").join("skills"),
+        |p| p.join(".codewhale").join("cache").join("skills"),
     )
 }
 

crates/tui/src/task_manager.rs

@@ -1648,9 +1648,9 @@ pub fn default_tasks_dir() -> PathBuf {
         return PathBuf::from(path);
     }
     if let Some(home) = dirs::home_dir() {
-        return home.join(".deepseek").join("tasks");
+        return home.join(".codewhale").join("tasks");
     }
-    PathBuf::from(".deepseek").join("tasks")
+    PathBuf::from(".codewhale").join("tasks")
 }
 
 /// Wait for a task to reach a terminal status (tests and API helpers).

crates/tui/src/tui/clipboard.rs

@@ -279,7 +279,7 @@ fn osc52_sequence(text: &str, in_tmux: bool) -> Result<String> {
 /// `<workspace>/clipboard-images/` if the home dir is unavailable.
 pub(crate) fn clipboard_images_dir(workspace: &Path) -> PathBuf {
     if let Some(home) = dirs::home_dir() {
-        return home.join(".deepseek").join("clipboard-images");
+        return home.join(".codewhale").join("clipboard-images");
     }
     workspace.join("clipboard-images")
 }

crates/tui/src/tui/file_frecency.rs

@@ -55,7 +55,7 @@ fn store() -> &'static Mutex<Store> {
 }
 
 fn default_path() -> Option<PathBuf> {
-    dirs::home_dir().map(|h| h.join(".deepseek").join("file-frecency.jsonl"))
+    dirs::home_dir().map(|h| h.join(".codewhale").join("file-frecency.jsonl"))
 }
 
 fn now_secs() -> u64 {

crates/tui/src/tui/onboarding/mod.rs

@@ -128,7 +128,11 @@ pub fn tips_lines(app: &App) -> Vec<ratatui::text::Line<'static>> {
 }
 
 pub fn default_marker_path() -> Option<PathBuf> {
-    dirs::home_dir().map(|home| home.join(".deepseek").join(".onboarded"))
+    dirs::home_dir().map(|home| {
+        let primary = home.join(".codewhale").join(".onboarded");
+        if primary.exists() { return primary; }
+        home.join(".deepseek").join(".onboarded")
+    })
 }
 
 pub fn is_onboarded() -> bool {