claudeup 4.1.0 → 4.2.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "claudeup",
-  "version": "4.1.0",
+  "version": "4.2.0",
   "description": "TUI tool for managing Claude Code plugins, MCPs, and configuration",
   "type": "module",
   "main": "src/main.tsx",

package/src/data/cli-tools.js

@@ -11,15 +11,15 @@ export const cliTools = [
         packageName: "claudeup",
     },
     {
-        name: "claudemem",
-        displayName: "Claudemem",
-        description: "Local semantic code search for Claude Code with vector embeddings",
-        installCommand: "npm install -g claude-codemem",
-        checkCommand: "claudemem --version",
-        website: "https://github.com/MadAppGang/claudemem",
+        name: "mnemex",
+        displayName: "Mnemex",
+        description: "AST-aware code search with PageRank, callers/callees, and semantic embeddings",
+        installCommand: "npm install -g mnemex",
+        checkCommand: "mnemex --version",
+        website: "https://github.com/MadAppGang/mnemex",
         category: "ai-coding",
         packageManager: "npm",
-        packageName: "claude-codemem",
+        packageName: "mnemex",
     },
     {
         name: "claudish",

package/src/data/cli-tools.ts

@@ -24,16 +24,16 @@ export const cliTools: CliTool[] = [
 		packageName: "claudeup",
 	},
 	{
-		name: "claudemem",
-		displayName: "Claudemem",
+		name: "mnemex",
+		displayName: "Mnemex",
 		description:
-			"Local semantic code search for Claude Code with vector embeddings",
-		installCommand: "npm install -g claude-codemem",
-		checkCommand: "claudemem --version",
-		website: "https://github.com/MadAppGang/claudemem",
+			"AST-aware code search with PageRank, callers/callees, and semantic embeddings",
+		installCommand: "npm install -g mnemex",
+		checkCommand: "mnemex --version",
+		website: "https://github.com/MadAppGang/mnemex",
 		category: "ai-coding",
 		packageManager: "npm",
-		packageName: "claude-codemem",
+		packageName: "mnemex",
 	},
 	{
 		name: "claudish",

package/src/services/claude-settings.js

@@ -418,6 +418,8 @@ export async function getMarketplaceAutoUpdate(marketplaceName) {
 // =============================================================================
 const OLD_MARKETPLACE_NAMES = ["mag-claude-plugins", "MadAppGang-claude-code"];
 const NEW_MARKETPLACE_NAME = "magus";
+const NEW_MARKETPLACE_REPO = "MadAppGang/magus";
+const OLD_MARKETPLACE_REPOS = ["MadAppGang/claude-code"];
 /**
  * Rename plugin keys in a Record from any old marketplace name to new.
  * e.g., "frontend@mag-claude-plugins" → "frontend@magus"
@@ -468,11 +470,24 @@ function migrateSettingsObject(settings) {
             const entry = settings.extraKnownMarketplaces[oldName];
             delete settings.extraKnownMarketplaces[oldName];
             if (!settings.extraKnownMarketplaces[NEW_MARKETPLACE_NAME]) {
-                settings.extraKnownMarketplaces[NEW_MARKETPLACE_NAME] = entry;
+                settings.extraKnownMarketplaces[NEW_MARKETPLACE_NAME] = {
+                    ...entry,
+                    source: {
+                        ...entry.source,
+                        repo: NEW_MARKETPLACE_REPO,
+                    },
+                };
             }
             total++;
         }
     }
+    // Fix stale repo URL on existing magus entry (e.g. key is "magus" but repo is still "MadAppGang/claude-code")
+    const magusEntry = settings.extraKnownMarketplaces?.[NEW_MARKETPLACE_NAME];
+    if (magusEntry?.source?.repo &&
+        OLD_MARKETPLACE_REPOS.includes(magusEntry.source.repo)) {
+        magusEntry.source.repo = NEW_MARKETPLACE_REPO;
+        total++;
+    }
     return total;
 }
 /**
@@ -639,6 +654,41 @@ export async function migrateMarketplaceRename(projectPath) {
     catch {
         /* skip if unreadable */
     }
+    // 6. Scan all known project settings (derived from ~/.claude/projects/ directory names)
+    try {
+        const projectsDir = path.join(os.homedir(), ".claude", "projects");
+        if (await fs.pathExists(projectsDir)) {
+            const entries = await fs.readdir(projectsDir);
+            const seenPaths = new Set();
+            // Current project (from step 1) already handled — skip it
+            const currentProject = projectPath || process.cwd();
+            seenPaths.add(currentProject);
+            for (const entry of entries) {
+                // Directory names encode paths: -Users-jack-dev-foo → /Users/jack/dev/foo
+                const decoded = entry.replace(/^-/, "/").replace(/-/g, "/");
+                if (seenPaths.has(decoded))
+                    continue;
+                seenPaths.add(decoded);
+                const settingsFile = path.join(decoded, ".claude", "settings.json");
+                try {
+                    if (await fs.pathExists(settingsFile)) {
+                        const raw = await fs.readJson(settingsFile);
+                        const count = migrateSettingsObject(raw);
+                        if (count > 0) {
+                            await fs.writeJson(settingsFile, raw, { spaces: 2 });
+                            result.projectMigrated += count;
+                        }
+                    }
+                }
+                catch {
+                    /* skip individual projects that fail */
+                }
+            }
+        }
+    }
+    catch {
+        /* non-fatal: cross-project scan is best-effort */
+    }
     return result;
 }
 /**

package/src/services/claude-settings.ts

@@ -635,6 +635,8 @@ export interface MarketplaceRecoveryResult {
 
 const OLD_MARKETPLACE_NAMES = ["mag-claude-plugins", "MadAppGang-claude-code"];
 const NEW_MARKETPLACE_NAME = "magus";
+const NEW_MARKETPLACE_REPO = "MadAppGang/magus";
+const OLD_MARKETPLACE_REPOS = ["MadAppGang/claude-code"];
 
 /**
  * Rename plugin keys in a Record from any old marketplace name to new.
@@ -690,12 +692,28 @@ function migrateSettingsObject(settings: ClaudeSettings): number {
 			const entry = settings.extraKnownMarketplaces[oldName];
 			delete settings.extraKnownMarketplaces[oldName];
 			if (!settings.extraKnownMarketplaces[NEW_MARKETPLACE_NAME]) {
-				settings.extraKnownMarketplaces[NEW_MARKETPLACE_NAME] = entry;
+				settings.extraKnownMarketplaces[NEW_MARKETPLACE_NAME] = {
+					...entry,
+					source: {
+						...entry.source,
+						repo: NEW_MARKETPLACE_REPO,
+					},
+				};
 			}
 			total++;
 		}
 	}
 
+	// Fix stale repo URL on existing magus entry (e.g. key is "magus" but repo is still "MadAppGang/claude-code")
+	const magusEntry = settings.extraKnownMarketplaces?.[NEW_MARKETPLACE_NAME];
+	if (
+		magusEntry?.source?.repo &&
+		OLD_MARKETPLACE_REPOS.includes(magusEntry.source.repo)
+	) {
+		magusEntry.source.repo = NEW_MARKETPLACE_REPO;
+		total++;
+	}
+
 	return total;
 }
 
@@ -885,6 +903,41 @@ export async function migrateMarketplaceRename(
 		/* skip if unreadable */
 	}
 
+	// 6. Scan all known project settings (derived from ~/.claude/projects/ directory names)
+	try {
+		const projectsDir = path.join(os.homedir(), ".claude", "projects");
+		if (await fs.pathExists(projectsDir)) {
+			const entries = await fs.readdir(projectsDir);
+			const seenPaths = new Set<string>();
+			// Current project (from step 1) already handled — skip it
+			const currentProject = projectPath || process.cwd();
+			seenPaths.add(currentProject);
+
+			for (const entry of entries) {
+				// Directory names encode paths: -Users-jack-dev-foo → /Users/jack/dev/foo
+				const decoded = entry.replace(/^-/, "/").replace(/-/g, "/");
+				if (seenPaths.has(decoded)) continue;
+				seenPaths.add(decoded);
+
+				const settingsFile = path.join(decoded, ".claude", "settings.json");
+				try {
+					if (await fs.pathExists(settingsFile)) {
+						const raw = await fs.readJson(settingsFile);
+						const count = migrateSettingsObject(raw);
+						if (count > 0) {
+							await fs.writeJson(settingsFile, raw, { spaces: 2 });
+							result.projectMigrated += count;
+						}
+					}
+				} catch {
+					/* skip individual projects that fail */
+				}
+			}
+		}
+	} catch {
+		/* non-fatal: cross-project scan is best-effort */
+	}
+
 	return result;
 }
 

package/src/ui/renderers/cliToolRenderers.js

@@ -1,33 +1,54 @@
 import { jsxs as _jsxs, jsx as _jsx } from "@opentui/react/jsx-runtime";
 import { theme } from "../theme.js";
+// ─── Helpers ────────────────────────────────────────────────────────────────
+function getUninstallHint(tool, method, brewFormula) {
+    switch (method) {
+        case "bun": return `bun remove -g ${tool.packageName}`;
+        case "npm": return `npm uninstall -g ${tool.packageName}`;
+        case "pnpm": return `pnpm remove -g ${tool.packageName}`;
+        case "yarn": return `yarn global remove ${tool.packageName}`;
+        case "brew": return `brew uninstall ${brewFormula || tool.name}`;
+        case "pip": return `pip uninstall ${tool.packageName}`;
+        default: return "";
+    }
+}
 // ─── Row renderer ──────────────────────────────────────────────────────────────
 export function renderCliToolRow(status, _index, isSelected) {
-    const { tool, installed, installedVersion, hasUpdate, checking } = status;
+    const { tool, installed, installedVersion, hasUpdate, checking, allMethods } = status;
+    const hasConflict = allMethods && allMethods.length > 1;
     let icon;
     let iconColor;
     if (!installed) {
         icon = "○";
         iconColor = theme.colors.muted;
     }
+    else if (hasConflict) {
+        icon = "!";
+        iconColor = theme.colors.danger;
+    }
     else if (hasUpdate) {
-        icon = "⬆";
+        icon = "*";
         iconColor = theme.colors.warning;
     }
     else {
         icon = "●";
         iconColor = theme.colors.success;
     }
-    const versionText = installedVersion ? `v${installedVersion}` : "";
+    const versionText = installedVersion ? ` v${installedVersion}` : "";
+    const methodTag = installed && allMethods?.length
+        ? ` ${allMethods.join("+")}`
+        : "";
     if (isSelected) {
-        return (_jsxs("text", { bg: theme.selection.bg, fg: theme.selection.fg, children: [" ", icon, " ", tool.displayName, " ", versionText, checking ? "..." : "", " "] }));
+        return (_jsxs("text", { bg: theme.selection.bg, fg: theme.selection.fg, children: [" ", icon, " ", tool.displayName, versionText, methodTag, checking ? " ..." : "", " "] }));
     }
-    return (_jsxs("text", { children: [_jsx("span", { fg: iconColor, children: icon }), _jsxs("span", { fg: theme.colors.text, children: [" ", tool.displayName] }), versionText ? _jsxs("span", { fg: theme.colors.success, children: [" ", versionText] }) : null, checking ? _jsx("span", { fg: theme.colors.muted, children: "..." }) : null] }));
+    return (_jsxs("text", { children: [_jsxs("span", { fg: iconColor, children: [" ", icon] }), _jsxs("span", { fg: theme.colors.text, children: [" ", tool.displayName] }), versionText ? _jsx("span", { fg: theme.colors.success, children: versionText }) : null, methodTag ? _jsx("span", { fg: hasConflict ? theme.colors.danger : theme.colors.dim, children: methodTag }) : null, checking ? _jsx("span", { fg: theme.colors.muted, children: " ..." }) : null] }));
 }
 // ─── Detail renderer ───────────────────────────────────────────────────────────
 export function renderCliToolDetail(status) {
     if (!status) {
         return (_jsx("box", { flexDirection: "column", alignItems: "center", justifyContent: "center", flexGrow: 1, children: _jsx("text", { fg: theme.colors.muted, children: "Select a tool to see details" }) }));
     }
-    const { tool, installed, installedVersion, latestVersion, hasUpdate, checking } = status;
-    return (_jsxs("box", { flexDirection: "column", children: [_jsxs("box", { marginBottom: 1, children: [_jsx("text", { fg: theme.colors.info, children: _jsxs("strong", { children: ["⚙ ", tool.displayName] }) }), hasUpdate ? _jsx("text", { fg: theme.colors.warning, children: " \u2B06" }) : null] }), _jsx("text", { fg: theme.colors.muted, children: tool.description }), _jsxs("box", { marginTop: 1, flexDirection: "column", children: [_jsxs("box", { children: [_jsx("text", { fg: theme.colors.muted, children: "Status " }), !installed ? (_jsx("text", { fg: theme.colors.muted, children: "○ Not installed" })) : checking ? (_jsx("text", { fg: theme.colors.success, children: "● Checking..." })) : hasUpdate ? (_jsx("text", { fg: theme.colors.warning, children: "● Update available" })) : (_jsx("text", { fg: theme.colors.success, children: "● Up to date" }))] }), installedVersion ? (_jsxs("box", { children: [_jsx("text", { fg: theme.colors.muted, children: "Installed " }), _jsxs("text", { fg: theme.colors.success, children: ["v", installedVersion] })] })) : null, latestVersion ? (_jsxs("box", { children: [_jsx("text", { fg: theme.colors.muted, children: "Latest " }), _jsxs("text", { fg: theme.colors.text, children: ["v", latestVersion] })] })) : null, _jsxs("box", { children: [_jsx("text", { fg: theme.colors.muted, children: "Website " }), _jsx("text", { fg: theme.colors.link, children: tool.website })] })] }), _jsx("box", { marginTop: 2, children: !installed ? (_jsxs("box", { children: [_jsxs("text", { bg: theme.colors.success, fg: "black", children: [" ", "Enter", " "] }), _jsx("text", { fg: theme.colors.muted, children: " Install" })] })) : hasUpdate ? (_jsxs("box", { children: [_jsxs("text", { bg: theme.colors.warning, fg: "black", children: [" ", "Enter", " "] }), _jsxs("text", { fg: theme.colors.muted, children: [" Update to v", latestVersion] })] })) : (_jsxs("box", { children: [_jsxs("text", { bg: theme.colors.muted, fg: "white", children: [" ", "Enter", " "] }), _jsx("text", { fg: theme.colors.muted, children: " Reinstall" })] })) })] }));
+    const { tool, installed, installedVersion, latestVersion, hasUpdate, checking, installMethod, allMethods, updateCommand, brewFormula } = status;
+    const hasConflict = allMethods && allMethods.length > 1;
+    return (_jsxs("box", { flexDirection: "column", children: [_jsxs("box", { marginBottom: 1, children: [_jsx("text", { fg: theme.colors.info, children: _jsxs("strong", { children: ["⚙ ", tool.displayName] }) }), hasUpdate ? _jsx("text", { fg: theme.colors.warning, children: " \u2B06" }) : null, hasConflict ? _jsx("text", { fg: theme.colors.danger, children: " !" }) : null] }), _jsx("text", { fg: theme.colors.muted, children: tool.description }), _jsxs("box", { marginTop: 1, flexDirection: "column", children: [_jsxs("box", { children: [_jsx("text", { fg: theme.colors.muted, children: "Status   " }), !installed ? (_jsx("text", { fg: theme.colors.muted, children: "○ Not installed" })) : checking ? (_jsx("text", { fg: theme.colors.success, children: "● Checking..." })) : hasUpdate ? (_jsx("text", { fg: theme.colors.warning, children: "● Update available" })) : (_jsx("text", { fg: theme.colors.success, children: "● Up to date" }))] }), installedVersion ? (_jsxs("box", { children: [_jsx("text", { fg: theme.colors.muted, children: "Version  " }), _jsxs("text", { children: [_jsxs("span", { fg: theme.colors.success, children: ["v", installedVersion] }), latestVersion && hasUpdate ? (_jsxs("span", { fg: theme.colors.warning, children: [" \u2192 v", latestVersion] })) : null] })] })) : latestVersion ? (_jsxs("box", { children: [_jsx("text", { fg: theme.colors.muted, children: "Latest   " }), _jsxs("text", { fg: theme.colors.text, children: ["v", latestVersion] })] })) : null, installed && updateCommand ? (_jsxs("box", { children: [_jsx("text", { fg: theme.colors.muted, children: "Update   " }), _jsx("text", { fg: theme.colors.accent, children: updateCommand })] })) : !installed ? (_jsxs("box", { children: [_jsx("text", { fg: theme.colors.muted, children: "Install  " }), _jsx("text", { fg: theme.colors.accent, children: tool.installCommand })] })) : null, _jsxs("box", { children: [_jsx("text", { fg: theme.colors.muted, children: "Website  " }), _jsx("text", { fg: theme.colors.link, children: tool.website })] })] }), hasConflict ? (_jsxs("box", { marginTop: 1, flexDirection: "column", children: [_jsx("box", { children: _jsx("text", { bg: theme.colors.danger, fg: "white", children: _jsxs("strong", { children: [" ", "Conflict: installed via ", allMethods.join(" + "), " "] }) }) }), _jsx("box", { marginTop: 1, children: _jsxs("text", { fg: theme.colors.muted, children: ["Multiple installs can cause version mismatches.", "\n", "Keep one, remove the rest:"] }) }), allMethods.map((method, i) => (_jsx("box", { children: _jsxs("text", { children: [_jsx("span", { fg: i === 0 ? theme.colors.success : theme.colors.danger, children: i === 0 ? "  ● keep  " : "  ○ remove " }), _jsx("span", { fg: theme.colors.warning, children: method }), i > 0 ? (_jsx("span", { fg: theme.colors.dim, children: `  ${getUninstallHint(tool, method, brewFormula)}` })) : (_jsx("span", { fg: theme.colors.dim, children: "  (active in PATH)" }))] }) }, method))), _jsxs("box", { marginTop: 1, children: [_jsxs("text", { bg: theme.colors.danger, fg: "white", children: [" ", "c", " "] }), _jsx("text", { fg: theme.colors.muted, children: " Resolve \u2014 pick which to keep" })] })] })) : null, _jsx("box", { marginTop: 2, flexDirection: "column", children: !installed ? (_jsxs("box", { children: [_jsxs("text", { bg: theme.colors.success, fg: "black", children: [" ", "Enter", " "] }), _jsx("text", { fg: theme.colors.muted, children: " Install" }), _jsxs("text", { fg: theme.colors.dim, children: ["  ", tool.installCommand] })] })) : hasUpdate ? (_jsxs("box", { children: [_jsxs("text", { bg: theme.colors.warning, fg: "black", children: [" ", "Enter", " "] }), _jsxs("text", { fg: theme.colors.muted, children: [" Update to v", latestVersion] })] })) : (_jsxs("box", { children: [_jsxs("text", { bg: theme.colors.muted, fg: "white", children: [" ", "Enter", " "] }), _jsx("text", { fg: theme.colors.muted, children: " Reinstall" })] })) })] }));
 }

package/src/ui/renderers/cliToolRenderers.tsx

@@ -4,6 +4,8 @@ import { theme } from "../theme.js";
 
 // ─── Status type ───────────────────────────────────────────────────────────────
 
+export type InstallMethod = "npm" | "bun" | "pnpm" | "yarn" | "brew" | "pip" | "unknown";
+
 export interface CliToolStatus {
   tool: CliTool;
   installed: boolean;
@@ -11,6 +13,24 @@ export interface CliToolStatus {
   latestVersion?: string;
   hasUpdate?: boolean;
   checking: boolean;
+  installMethod?: InstallMethod;
+  allMethods?: InstallMethod[];
+  updateCommand?: string;
+  brewFormula?: string;
+}
+
+// ─── Helpers ────────────────────────────────────────────────────────────────
+
+function getUninstallHint(tool: CliTool, method: InstallMethod, brewFormula?: string): string {
+  switch (method) {
+    case "bun": return `bun remove -g ${tool.packageName}`;
+    case "npm": return `npm uninstall -g ${tool.packageName}`;
+    case "pnpm": return `pnpm remove -g ${tool.packageName}`;
+    case "yarn": return `yarn global remove ${tool.packageName}`;
+    case "brew": return `brew uninstall ${brewFormula || tool.name}`;
+    case "pip": return `pip uninstall ${tool.packageName}`;
+    default: return "";
+  }
 }
 
 // ─── Row renderer ──────────────────────────────────────────────────────────────
@@ -20,7 +40,8 @@ export function renderCliToolRow(
   _index: number,
   isSelected: boolean,
 ): React.ReactNode {
-  const { tool, installed, installedVersion, hasUpdate, checking } = status;
+  const { tool, installed, installedVersion, hasUpdate, checking, allMethods } = status;
+  const hasConflict = allMethods && allMethods.length > 1;
 
   let icon: string;
   let iconColor: string;
@@ -28,32 +49,38 @@ export function renderCliToolRow(
   if (!installed) {
     icon = "○";
     iconColor = theme.colors.muted;
+  } else if (hasConflict) {
+    icon = "!";
+    iconColor = theme.colors.danger;
   } else if (hasUpdate) {
-    icon = "⬆";
+    icon = "*";
     iconColor = theme.colors.warning;
   } else {
     icon = "●";
     iconColor = theme.colors.success;
   }
 
-  const versionText = installedVersion ? `v${installedVersion}` : "";
+  const versionText = installedVersion ? ` v${installedVersion}` : "";
+  const methodTag = installed && allMethods?.length
+    ? ` ${allMethods.join("+")}`
+    : "";
 
   if (isSelected) {
     return (
       <text bg={theme.selection.bg} fg={theme.selection.fg}>
-        {" "}
-        {icon} {tool.displayName} {versionText}
-        {checking ? "..." : ""}{" "}
+        {" "}{icon} {tool.displayName}{versionText}{methodTag}
+        {checking ? " ..." : ""}{" "}
       </text>
     );
   }
 
   return (
     <text>
-      <span fg={iconColor}>{icon}</span>
+      <span fg={iconColor}> {icon}</span>
       <span fg={theme.colors.text}> {tool.displayName}</span>
-      {versionText ? <span fg={theme.colors.success}> {versionText}</span> : null}
-      {checking ? <span fg={theme.colors.muted}>{"..."}</span> : null}
+      {versionText ? <span fg={theme.colors.success}>{versionText}</span> : null}
+      {methodTag ? <span fg={hasConflict ? theme.colors.danger : theme.colors.dim}>{methodTag}</span> : null}
+      {checking ? <span fg={theme.colors.muted}>{" ..."}</span> : null}
     </text>
   );
 }
@@ -76,9 +103,11 @@ export function renderCliToolDetail(
     );
   }
 
-  const { tool, installed, installedVersion, latestVersion, hasUpdate, checking } =
+  const { tool, installed, installedVersion, latestVersion, hasUpdate, checking, installMethod, allMethods, updateCommand, brewFormula } =
     status;
 
+  const hasConflict = allMethods && allMethods.length > 1;
+
   return (
     <box flexDirection="column">
       <box marginBottom={1}>
@@ -86,13 +115,14 @@ export function renderCliToolDetail(
           <strong>{"⚙ "}{tool.displayName}</strong>
         </text>
         {hasUpdate ? <text fg={theme.colors.warning}> ⬆</text> : null}
+        {hasConflict ? <text fg={theme.colors.danger}> !</text> : null}
       </box>
 
       <text fg={theme.colors.muted}>{tool.description}</text>
 
       <box marginTop={1} flexDirection="column">
         <box>
-          <text fg={theme.colors.muted}>{"Status "}</text>
+          <text fg={theme.colors.muted}>{"Status   "}</text>
           {!installed ? (
             <text fg={theme.colors.muted}>{"○ Not installed"}</text>
           ) : checking ? (
@@ -105,45 +135,89 @@ export function renderCliToolDetail(
         </box>
         {installedVersion ? (
           <box>
-            <text fg={theme.colors.muted}>{"Installed "}</text>
-            <text fg={theme.colors.success}>v{installedVersion}</text>
+            <text fg={theme.colors.muted}>{"Version  "}</text>
+            <text>
+              <span fg={theme.colors.success}>v{installedVersion}</span>
+              {latestVersion && hasUpdate ? (
+                <span fg={theme.colors.warning}> → v{latestVersion}</span>
+              ) : null}
+            </text>
+          </box>
+        ) : latestVersion ? (
+          <box>
+            <text fg={theme.colors.muted}>{"Latest   "}</text>
+            <text fg={theme.colors.text}>v{latestVersion}</text>
           </box>
         ) : null}
-        {latestVersion ? (
+        {installed && updateCommand ? (
           <box>
-            <text fg={theme.colors.muted}>{"Latest "}</text>
-            <text fg={theme.colors.text}>v{latestVersion}</text>
+            <text fg={theme.colors.muted}>{"Update   "}</text>
+            <text fg={theme.colors.accent}>{updateCommand}</text>
+          </box>
+        ) : !installed ? (
+          <box>
+            <text fg={theme.colors.muted}>{"Install  "}</text>
+            <text fg={theme.colors.accent}>{tool.installCommand}</text>
           </box>
         ) : null}
         <box>
-          <text fg={theme.colors.muted}>{"Website "}</text>
+          <text fg={theme.colors.muted}>{"Website  "}</text>
           <text fg={theme.colors.link}>{tool.website}</text>
         </box>
       </box>
 
-      <box marginTop={2}>
-        {!installed ? (
+      {/* Conflict warning */}
+      {hasConflict ? (
+        <box marginTop={1} flexDirection="column">
           <box>
-            <text bg={theme.colors.success} fg="black">
-              {" "}
-              Enter{" "}
+            <text bg={theme.colors.danger} fg="white">
+              <strong>{" "}Conflict: installed via {allMethods.join(" + ")}{" "}</strong>
+            </text>
+          </box>
+          <box marginTop={1}>
+            <text fg={theme.colors.muted}>
+              Multiple installs can cause version mismatches.
+              {"\n"}Keep one, remove the rest:
             </text>
+          </box>
+          {allMethods.map((method, i) => (
+            <box key={method}>
+              <text>
+                <span fg={i === 0 ? theme.colors.success : theme.colors.danger}>
+                  {i === 0 ? "  ● keep  " : "  ○ remove "}
+                </span>
+                <span fg={theme.colors.warning}>{method}</span>
+                {i > 0 ? (
+                  <span fg={theme.colors.dim}>{`  ${getUninstallHint(tool, method, brewFormula)}`}</span>
+                ) : (
+                  <span fg={theme.colors.dim}>  (active in PATH)</span>
+                )}
+              </text>
+            </box>
+          ))}
+          <box marginTop={1}>
+            <text bg={theme.colors.danger} fg="white">{" "}c{" "}</text>
+            <text fg={theme.colors.muted}> Resolve — pick which to keep</text>
+          </box>
+        </box>
+      ) : null}
+
+      {/* Actions */}
+      <box marginTop={2} flexDirection="column">
+        {!installed ? (
+          <box>
+            <text bg={theme.colors.success} fg="black">{" "}Enter{" "}</text>
             <text fg={theme.colors.muted}> Install</text>
+            <text fg={theme.colors.dim}>  {tool.installCommand}</text>
           </box>
         ) : hasUpdate ? (
           <box>
-            <text bg={theme.colors.warning} fg="black">
-              {" "}
-              Enter{" "}
-            </text>
+            <text bg={theme.colors.warning} fg="black">{" "}Enter{" "}</text>
             <text fg={theme.colors.muted}> Update to v{latestVersion}</text>
           </box>
         ) : (
           <box>
-            <text bg={theme.colors.muted} fg="white">
-              {" "}
-              Enter{" "}
-            </text>
+            <text bg={theme.colors.muted} fg="white">{" "}Enter{" "}</text>
             <text fg={theme.colors.muted}> Reinstall</text>
           </box>
         )}

package/src/ui/renderers/pluginRenderers.js

@@ -82,7 +82,7 @@ function pluginDetail(item) {
         plugin.localScope?.enabled;
     // Orphaned/deprecated plugin
     if (plugin.isOrphaned) {
-        return (_jsxs("box", { flexDirection: "column", children: [_jsx("box", { justifyContent: "center", children: _jsx("text", { bg: theme.colors.warning, fg: "black", children: _jsxs("strong", { children: [" ", plugin.name, " \u2014 DEPRECATED "] }) }) }), _jsx("box", { marginTop: 1, children: _jsx("text", { fg: theme.colors.warning, children: "This plugin is no longer in the marketplace." }) }), _jsx("box", { marginTop: 1, children: _jsx("text", { fg: theme.colors.muted, children: "It was removed from the marketplace but still referenced in your settings. Press d to uninstall and clean up." }) }), isInstalled ? (_jsx(ActionHints, { hints: [{ key: "d", label: "Uninstall (recommended)", tone: "danger" }] })) : null] }));
+        return (_jsxs("box", { flexDirection: "column", children: [_jsx("box", { justifyContent: "center", children: _jsx("text", { bg: theme.colors.warning, fg: "black", children: _jsxs("strong", { children: [" ", plugin.name, " \u2014 DEPRECATED "] }) }) }), _jsx("box", { marginTop: 1, children: _jsx("text", { fg: theme.colors.warning, children: "This plugin is no longer in the marketplace." }) }), _jsx("box", { marginTop: 1, children: _jsx("text", { fg: theme.colors.muted, children: "It was removed from the marketplace but still referenced in your settings. Press d to uninstall and clean up." }) }), _jsx(ActionHints, { hints: [{ key: "d", label: isInstalled ? "Remove from all scopes" : "Clean up stale reference", tone: "danger" }] })] }));
     }
     // Build component counts
     const components = [];

package/src/ui/renderers/pluginRenderers.tsx

@@ -191,11 +191,9 @@ function pluginDetail(item: PluginPluginItem): React.ReactNode {
             uninstall and clean up.
           </text>
         </box>
-        {isInstalled ? (
-          <ActionHints
-            hints={[{ key: "d", label: "Uninstall (recommended)", tone: "danger" }]}
-          />
-        ) : null}
+        <ActionHints
+          hints={[{ key: "d", label: isInstalled ? "Remove from all scopes" : "Clean up stale reference", tone: "danger" }]}
+        />
       </box>
     );
   }

package/src/ui/screens/CliToolsScreen.js

@@ -1,6 +1,6 @@
 import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "@opentui/react/jsx-runtime";
 import { useEffect, useCallback, useState, useRef } from "react";
-import { exec, execSync } from "child_process";
+import { exec } from "child_process";
 import { promisify } from "util";
 import { useApp, useModal } from "../state/AppContext.js";
 import { useDimensions } from "../state/DimensionsContext.js";
@@ -22,17 +22,94 @@ function parseVersion(versionOutput) {
     const match = versionOutput.match(/v?(\d+\.\d+\.\d+(?:-[\w.]+)?)/);
     return match ? match[1] : undefined;
 }
-async function isInstalledViaHomebrew(toolName) {
+function methodFromPath(binPath) {
+    if (binPath.includes("/.bun/"))
+        return "bun";
+    if (binPath.includes("/homebrew/") || binPath.includes("/Cellar/"))
+        return "brew";
+    if (binPath.includes("/.local/share/claude") || binPath.includes("/.local/bin/claude"))
+        return "npm";
+    if (binPath.includes("/.nvm/") || binPath.includes("/node_modules/"))
+        return "npm";
+    if (binPath.includes("/.local/share/pnpm") || binPath.includes("/pnpm/"))
+        return "pnpm";
+    if (binPath.includes("/.yarn/"))
+        return "yarn";
+    return null;
+}
+/** Extract brew formula name from a Cellar symlink target like ../Cellar/gemini-cli/0.35.2/bin/gemini */
+function extractBrewFormula(binPath, linkTarget) {
+    // Try symlink target first: ../Cellar/{formula}/{version}/...
+    const cellarMatch = linkTarget.match(/Cellar\/([^/]+)\//);
+    if (cellarMatch)
+        return cellarMatch[1];
+    // Try binary path: /opt/homebrew/Cellar/{formula}/...
+    const pathMatch = binPath.match(/Cellar\/([^/]+)\//);
+    if (pathMatch)
+        return pathMatch[1];
+    return undefined;
+}
+async function detectInstallMethods(tool) {
+    const fallback = tool.packageManager === "pip" ? "pip" : "unknown";
     try {
-        const { stdout } = await execAsync("brew list --formula 2>/dev/null", {
-            timeout: 2000,
+        // which -a returns all matching binaries across PATH
+        const { stdout } = await execAsync(`which -a ${tool.name} 2>/dev/null`, {
+            timeout: 3000,
             shell: "/bin/bash",
         });
-        const formulas = stdout.trim().split("\n");
-        return formulas.some((f) => f.trim() === toolName);
+        const paths = stdout.trim().split("\n").filter((p) => p && !p.includes("aliased"));
+        if (paths.length === 0)
+            return { primary: fallback, all: [] };
+        const methods = [];
+        let brewFormula;
+        for (const binPath of paths) {
+            let method = methodFromPath(binPath);
+            let linkTarget = "";
+            // Check symlink target
+            try {
+                const { stdout: lt } = await execAsync(`readlink "${binPath}" 2>/dev/null || true`, { timeout: 2000, shell: "/bin/bash" });
+                linkTarget = lt.trim();
+                if (!method)
+                    method = methodFromPath(linkTarget);
+            }
+            catch {
+                // ignore
+            }
+            // Detect brew formula name
+            if (method === "brew" && !brewFormula) {
+                brewFormula = extractBrewFormula(binPath, linkTarget);
+            }
+            if (method && !methods.includes(method))
+                methods.push(method);
+        }
+        if (methods.length === 0)
+            return { primary: fallback, all: [] };
+        return { primary: methods[0], all: methods, brewFormula };
     }
     catch {
-        return false;
+        return { primary: fallback, all: [] };
+    }
+}
+function getUninstallCommand(tool, method, brewFormula) {
+    switch (method) {
+        case "bun": return `bun remove -g ${tool.packageName}`;
+        case "npm": return `npm uninstall -g ${tool.packageName}`;
+        case "pnpm": return `pnpm remove -g ${tool.packageName}`;
+        case "yarn": return `yarn global remove ${tool.packageName}`;
+        case "brew": return `brew uninstall ${brewFormula || tool.name}`;
+        case "pip": return `pip uninstall -y ${tool.packageName}`;
+        default: return "";
+    }
+}
+function getUpdateCommand(tool, method, brewFormula) {
+    switch (method) {
+        case "bun": return `bun install -g ${tool.packageName}`;
+        case "npm": return `npm install -g ${tool.packageName}`;
+        case "pnpm": return `pnpm install -g ${tool.packageName}`;
+        case "yarn": return `yarn global add ${tool.packageName}`;
+        case "brew": return `brew upgrade ${brewFormula || tool.name}`;
+        case "pip": return tool.installCommand;
+        default: return tool.installCommand;
     }
 }
 async function getInstalledVersion(tool) {
@@ -109,20 +186,24 @@ export function CliToolsScreen() {
     const fetchVersionInfo = useCallback(async () => {
         for (let i = 0; i < cliTools.length; i++) {
             const tool = cliTools[i];
-            getInstalledVersion(tool).then((version) => {
+            // Run all checks in parallel, then update with all results
+            Promise.all([
+                getInstalledVersion(tool),
+                getLatestVersion(tool),
+                detectInstallMethods(tool),
+            ]).then(([version, latest, info]) => {
                 updateToolStatus(i, {
                     installedVersion: version,
                     installed: version !== undefined,
-                });
-            });
-            getLatestVersion(tool).then((latest) => {
-                const current = statusesRef.current[i];
-                updateToolStatus(i, {
                     latestVersion: latest,
                     checking: false,
-                    hasUpdate: current.installedVersion && latest
-                        ? compareVersions(current.installedVersion, latest) < 0
+                    hasUpdate: version && latest
+                        ? compareVersions(version, latest) < 0
                         : false,
+                    installMethod: version ? info.primary : undefined,
+                    allMethods: version && info.all.length > 1 ? info.all : undefined,
+                    updateCommand: version ? getUpdateCommand(tool, info.primary, info.brewFormula) : undefined,
+                    brewFormula: info.brewFormula,
                 });
             });
         }
@@ -151,7 +232,10 @@ export function CliToolsScreen() {
         else if (event.name === "a") {
             handleUpdateAll();
         }
-        else if (event.name === "enter") {
+        else if (event.name === "c") {
+            handleResolveConflict();
+        }
+        else if (event.name === "enter" || event.name === "return") {
             handleInstall();
         }
     });
@@ -166,35 +250,66 @@ export function CliToolsScreen() {
         cacheInitialized = false;
         fetchVersionInfo();
     };
+    const runCommand = async (command) => {
+        try {
+            await execAsync(command, {
+                shell: "/bin/bash",
+                timeout: 60000,
+            });
+            return { ok: true };
+        }
+        catch (err) {
+            const msg = err instanceof Error ? err.message : String(err);
+            return { ok: false, error: msg };
+        }
+    };
     const handleInstall = async () => {
         const status = toolStatuses[cliToolsState.selectedIndex];
         if (!status)
             return;
-        const { tool, installed, hasUpdate } = status;
+        const { tool, installed, hasUpdate, updateCommand } = status;
         const action = !installed ? "Installing" : hasUpdate ? "Updating" : "Reinstalling";
-        const viaHomebrew = installed
-            ? await isInstalledViaHomebrew(tool.name)
-            : false;
-        const command = !installed
-            ? tool.installCommand
-            : viaHomebrew
-                ? `brew upgrade ${tool.name}`
-                : tool.installCommand;
+        const command = installed && updateCommand ? updateCommand : tool.installCommand;
         modal.loading(`${action} ${tool.displayName}...`);
-        try {
-            execSync(command, {
-                encoding: "utf-8",
-                stdio: "pipe",
-                shell: "/bin/bash",
-            });
-            modal.hideModal();
+        const result = await runCommand(command);
+        modal.hideModal();
+        if (result.ok) {
             handleRefresh();
         }
-        catch (error) {
-            modal.hideModal();
+        else {
             await modal.message("Error", `Failed to ${action.toLowerCase()} ${tool.displayName}.\n\nTry running manually:\n${command}`, "error");
         }
     };
+    const handleResolveConflict = async () => {
+        const status = toolStatuses[cliToolsState.selectedIndex];
+        if (!status || !status.allMethods || status.allMethods.length < 2)
+            return;
+        const { tool, allMethods, installMethod, brewFormula } = status;
+        // Let user pick which install to keep
+        const options = allMethods.map((method) => ({
+            label: `Keep ${method}${method === installMethod ? " (active)" : ""}, remove others`,
+            value: method,
+        }));
+        const keep = await modal.select(`Resolve ${tool.displayName} conflict`, `Installed via ${allMethods.join(" + ")}. Which to keep?`, options);
+        if (keep === null)
+            return;
+        const toRemove = allMethods.filter((m) => m !== keep);
+        modal.loading(`Removing ${toRemove.join(", ")} install(s)...`);
+        const errors = [];
+        for (const method of toRemove) {
+            const cmd = getUninstallCommand(tool, method, brewFormula);
+            if (!cmd)
+                continue;
+            const result = await runCommand(cmd);
+            if (!result.ok)
+                errors.push(`${method}: ${cmd}`);
+        }
+        modal.hideModal();
+        if (errors.length > 0) {
+            await modal.message("Partial", `Some removals failed. Try manually:\n\n${errors.join("\n")}`, "error");
+        }
+        handleRefresh();
+    };
     const handleUpdateAll = async () => {
         const updatable = toolStatuses.filter((s) => s.hasUpdate);
         if (updatable.length === 0) {
@@ -203,20 +318,8 @@ export function CliToolsScreen() {
         }
         modal.loading(`Updating ${updatable.length} tool(s)...`);
         for (const status of updatable) {
-            const viaHomebrew = await isInstalledViaHomebrew(status.tool.name);
-            const command = viaHomebrew
-                ? `brew upgrade ${status.tool.name}`
-                : status.tool.installCommand;
-            try {
-                execSync(command, {
-                    encoding: "utf-8",
-                    stdio: "pipe",
-                    shell: "/bin/bash",
-                });
-            }
-            catch {
-                // Continue with other updates
-            }
+            const command = status.updateCommand || status.tool.installCommand;
+            await runCommand(command);
         }
         modal.hideModal();
         handleRefresh();
@@ -225,6 +328,6 @@ export function CliToolsScreen() {
     const installedCount = toolStatuses.filter((s) => s.installed).length;
     const updateCount = toolStatuses.filter((s) => s.hasUpdate).length;
     const statusContent = (_jsxs("text", { children: [_jsx("span", { fg: "gray", children: "Installed: " }), _jsxs("span", { fg: "cyan", children: [installedCount, "/", toolStatuses.length] }), updateCount > 0 && (_jsxs(_Fragment, { children: [_jsx("span", { fg: "gray", children: " \u2502 Updates: " }), _jsx("span", { fg: "yellow", children: updateCount })] }))] }));
-    return (_jsx(ScreenLayout, { title: "claudeup CLI Tools", currentScreen: "cli-tools", statusLine: statusContent, footerHints: "\u2191\u2193:nav \u2502 Enter:install \u2502 a:update all \u2502 r:refresh", listPanel: _jsx(ScrollableList, { items: toolStatuses, selectedIndex: cliToolsState.selectedIndex, renderItem: renderCliToolRow, maxHeight: dimensions.listPanelHeight }), detailPanel: renderCliToolDetail(selectedStatus) }));
+    return (_jsx(ScreenLayout, { title: "claudeup CLI Tools", currentScreen: "cli-tools", statusLine: statusContent, footerHints: "Enter:install \u2502 a:update all \u2502 c:fix conflict \u2502 r:refresh", listPanel: _jsx(ScrollableList, { items: toolStatuses, selectedIndex: cliToolsState.selectedIndex, renderItem: renderCliToolRow, maxHeight: dimensions.listPanelHeight }), detailPanel: renderCliToolDetail(selectedStatus) }));
 }
 export default CliToolsScreen;

package/src/ui/screens/CliToolsScreen.tsx

@@ -1,5 +1,5 @@
 import React, { useEffect, useCallback, useState, useRef } from "react";
-import { exec, execSync } from "child_process";
+import { exec } from "child_process";
 import { promisify } from "util";
 import { useApp, useModal } from "../state/AppContext.js";
 import { useDimensions } from "../state/DimensionsContext.js";
@@ -11,6 +11,7 @@ import {
 	renderCliToolRow,
 	renderCliToolDetail,
 	type CliToolStatus,
+	type InstallMethod,
 } from "../renderers/cliToolRenderers.js";
 
 const execAsync = promisify(exec);
@@ -31,19 +32,105 @@ function parseVersion(versionOutput: string): string | undefined {
 	return match ? match[1] : undefined;
 }
 
-async function isInstalledViaHomebrew(toolName: string): Promise<boolean> {
+function methodFromPath(binPath: string): InstallMethod | null {
+	if (binPath.includes("/.bun/")) return "bun";
+	if (binPath.includes("/homebrew/") || binPath.includes("/Cellar/")) return "brew";
+	if (binPath.includes("/.local/share/claude") || binPath.includes("/.local/bin/claude")) return "npm";
+	if (binPath.includes("/.nvm/") || binPath.includes("/node_modules/")) return "npm";
+	if (binPath.includes("/.local/share/pnpm") || binPath.includes("/pnpm/")) return "pnpm";
+	if (binPath.includes("/.yarn/")) return "yarn";
+	return null;
+}
+
+interface InstallInfo {
+	primary: InstallMethod;
+	all: InstallMethod[];
+	brewFormula?: string;
+}
+
+/** Extract brew formula name from a Cellar symlink target like ../Cellar/gemini-cli/0.35.2/bin/gemini */
+function extractBrewFormula(binPath: string, linkTarget: string): string | undefined {
+	// Try symlink target first: ../Cellar/{formula}/{version}/...
+	const cellarMatch = linkTarget.match(/Cellar\/([^/]+)\//);
+	if (cellarMatch) return cellarMatch[1];
+	// Try binary path: /opt/homebrew/Cellar/{formula}/...
+	const pathMatch = binPath.match(/Cellar\/([^/]+)\//);
+	if (pathMatch) return pathMatch[1];
+	return undefined;
+}
+
+async function detectInstallMethods(
+	tool: import("../../data/cli-tools.js").CliTool,
+): Promise<InstallInfo> {
+	const fallback = tool.packageManager === "pip" ? "pip" : "unknown";
 	try {
-		const { stdout } = await execAsync("brew list --formula 2>/dev/null", {
-			timeout: 2000,
+		// which -a returns all matching binaries across PATH
+		const { stdout } = await execAsync(`which -a ${tool.name} 2>/dev/null`, {
+			timeout: 3000,
 			shell: "/bin/bash",
 		});
-		const formulas = stdout.trim().split("\n");
-		return formulas.some((f) => f.trim() === toolName);
+		const paths = stdout.trim().split("\n").filter((p) => p && !p.includes("aliased"));
+		if (paths.length === 0) return { primary: fallback as InstallMethod, all: [] };
+
+		const methods: InstallMethod[] = [];
+		let brewFormula: string | undefined;
+
+		for (const binPath of paths) {
+			let method = methodFromPath(binPath);
+			let linkTarget = "";
+
+			// Check symlink target
+			try {
+				const { stdout: lt } = await execAsync(
+					`readlink "${binPath}" 2>/dev/null || true`,
+					{ timeout: 2000, shell: "/bin/bash" },
+				);
+				linkTarget = lt.trim();
+				if (!method) method = methodFromPath(linkTarget);
+			} catch {
+				// ignore
+			}
+
+			// Detect brew formula name
+			if (method === "brew" && !brewFormula) {
+				brewFormula = extractBrewFormula(binPath, linkTarget);
+			}
+
+			if (method && !methods.includes(method)) methods.push(method);
+		}
+
+		if (methods.length === 0) return { primary: fallback as InstallMethod, all: [] };
+		return { primary: methods[0]!, all: methods, brewFormula };
 	} catch {
-		return false;
+		return { primary: fallback as InstallMethod, all: [] };
+	}
+}
+
+function getUninstallCommand(tool: import("../../data/cli-tools.js").CliTool, method: InstallMethod, brewFormula?: string): string {
+	switch (method) {
+		case "bun": return `bun remove -g ${tool.packageName}`;
+		case "npm": return `npm uninstall -g ${tool.packageName}`;
+		case "pnpm": return `pnpm remove -g ${tool.packageName}`;
+		case "yarn": return `yarn global remove ${tool.packageName}`;
+		case "brew": return `brew uninstall ${brewFormula || tool.name}`;
+		case "pip": return `pip uninstall -y ${tool.packageName}`;
+		default: return "";
 	}
 }
 
+function getUpdateCommand(tool: import("../../data/cli-tools.js").CliTool, method: InstallMethod, brewFormula?: string): string {
+	switch (method) {
+		case "bun": return `bun install -g ${tool.packageName}`;
+		case "npm": return `npm install -g ${tool.packageName}`;
+		case "pnpm": return `pnpm install -g ${tool.packageName}`;
+		case "yarn": return `yarn global add ${tool.packageName}`;
+		case "brew": return `brew upgrade ${brewFormula || tool.name}`;
+		case "pip": return tool.installCommand;
+		default: return tool.installCommand;
+	}
+}
+
+
 async function getInstalledVersion(
 	tool: import("../../data/cli-tools.js").CliTool,
 ): Promise<string | undefined> {
@@ -138,22 +225,26 @@ export function CliToolsScreen() {
 	const fetchVersionInfo = useCallback(async () => {
 		for (let i = 0; i < cliTools.length; i++) {
 			const tool = cliTools[i]!;
-			getInstalledVersion(tool).then((version) => {
+
+			// Run all checks in parallel, then update with all results
+			Promise.all([
+				getInstalledVersion(tool),
+				getLatestVersion(tool),
+				detectInstallMethods(tool),
+			]).then(([version, latest, info]) => {
 				updateToolStatus(i, {
 					installedVersion: version,
 					installed: version !== undefined,
-				});
-			});
-
-			getLatestVersion(tool).then((latest) => {
-				const current = statusesRef.current[i]!;
-				updateToolStatus(i, {
 					latestVersion: latest,
 					checking: false,
 					hasUpdate:
-						current.installedVersion && latest
-							? compareVersions(current.installedVersion, latest) < 0
+						version && latest
+							? compareVersions(version, latest) < 0
 							: false,
+					installMethod: version ? info.primary : undefined,
+					allMethods: version && info.all.length > 1 ? info.all : undefined,
+					updateCommand: version ? getUpdateCommand(tool, info.primary, info.brewFormula) : undefined,
+					brewFormula: info.brewFormula,
 				});
 			});
 		}
@@ -183,7 +274,9 @@ export function CliToolsScreen() {
 			handleRefresh();
 		} else if (event.name === "a") {
 			handleUpdateAll();
-		} else if (event.name === "enter") {
+		} else if (event.name === "c") {
+			handleResolveConflict();
+		} else if (event.name === "enter" || event.name === "return") {
 			handleInstall();
 		}
 	});
@@ -202,34 +295,34 @@ export function CliToolsScreen() {
 		fetchVersionInfo();
 	};
 
+	const runCommand = async (command: string): Promise<{ ok: boolean; error?: string }> => {
+		try {
+			await execAsync(command, {
+				shell: "/bin/bash",
+				timeout: 60000,
+			});
+			return { ok: true };
+		} catch (err) {
+			const msg = err instanceof Error ? err.message : String(err);
+			return { ok: false, error: msg };
+		}
+	};
+
 	const handleInstall = async () => {
 		const status = toolStatuses[cliToolsState.selectedIndex];
 		if (!status) return;
 
-		const { tool, installed, hasUpdate } = status;
+		const { tool, installed, hasUpdate, updateCommand } = status;
 		const action = !installed ? "Installing" : hasUpdate ? "Updating" : "Reinstalling";
-
-		const viaHomebrew = installed
-			? await isInstalledViaHomebrew(tool.name)
-			: false;
-
-		const command = !installed
-			? tool.installCommand
-			: viaHomebrew
-				? `brew upgrade ${tool.name}`
-				: tool.installCommand;
+		const command = installed && updateCommand ? updateCommand : tool.installCommand;
 
 		modal.loading(`${action} ${tool.displayName}...`);
-		try {
-			execSync(command, {
-				encoding: "utf-8",
-				stdio: "pipe",
-				shell: "/bin/bash",
-			});
-			modal.hideModal();
+		const result = await runCommand(command);
+		modal.hideModal();
+
+		if (result.ok) {
 			handleRefresh();
-		} catch (error) {
-			modal.hideModal();
+		} else {
 			await modal.message(
 				"Error",
 				`Failed to ${action.toLowerCase()} ${tool.displayName}.\n\nTry running manually:\n${command}`,
@@ -238,6 +331,49 @@ export function CliToolsScreen() {
 		}
 	};
 
+	const handleResolveConflict = async () => {
+		const status = toolStatuses[cliToolsState.selectedIndex];
+		if (!status || !status.allMethods || status.allMethods.length < 2) return;
+
+		const { tool, allMethods, installMethod, brewFormula } = status;
+
+		// Let user pick which install to keep
+		const options = allMethods.map((method) => ({
+			label: `Keep ${method}${method === installMethod ? " (active)" : ""}, remove others`,
+			value: method,
+		}));
+
+		const keep = await modal.select(
+			`Resolve ${tool.displayName} conflict`,
+			`Installed via ${allMethods.join(" + ")}. Which to keep?`,
+			options,
+		);
+		if (keep === null) return;
+
+		const toRemove = allMethods.filter((m) => m !== keep);
+		modal.loading(`Removing ${toRemove.join(", ")} install(s)...`);
+
+		const errors: string[] = [];
+		for (const method of toRemove) {
+			const cmd = getUninstallCommand(tool, method, brewFormula);
+			if (!cmd) continue;
+			const result = await runCommand(cmd);
+			if (!result.ok) errors.push(`${method}: ${cmd}`);
+		}
+
+		modal.hideModal();
+
+		if (errors.length > 0) {
+			await modal.message(
+				"Partial",
+				`Some removals failed. Try manually:\n\n${errors.join("\n")}`,
+				"error",
+			);
+		}
+
+		handleRefresh();
+	};
+
 	const handleUpdateAll = async () => {
 		const updatable = toolStatuses.filter((s) => s.hasUpdate);
 		if (updatable.length === 0) {
@@ -248,19 +384,8 @@ export function CliToolsScreen() {
 		modal.loading(`Updating ${updatable.length} tool(s)...`);
 
 		for (const status of updatable) {
-			const viaHomebrew = await isInstalledViaHomebrew(status.tool.name);
-			const command = viaHomebrew
-				? `brew upgrade ${status.tool.name}`
-				: status.tool.installCommand;
-			try {
-				execSync(command, {
-					encoding: "utf-8",
-					stdio: "pipe",
-					shell: "/bin/bash",
-				});
-			} catch {
-				// Continue with other updates
-			}
+			const command = status.updateCommand || status.tool.installCommand;
+			await runCommand(command);
 		}
 
 		modal.hideModal();
@@ -291,7 +416,7 @@ export function CliToolsScreen() {
 			title="claudeup CLI Tools"
 			currentScreen="cli-tools"
 			statusLine={statusContent}
-			footerHints="↑↓:nav │ Enter:install │ a:update all │ r:refresh"
+			footerHints="Enter:install │ a:update all │ c:fix conflict │ r:refresh"
 			listPanel={
 				<ScrollableList
 					items={toolStatuses}

package/src/ui/screens/PluginsScreen.js

@@ -198,6 +198,8 @@ export function PluginsScreen() {
             handleScopeToggle("project");
         else if (event.name === "l")
             handleScopeToggle("local");
+        else if (event.name === "d")
+            handleRemoveDeprecated();
         else if (event.name === "U")
             handleUpdate();
         else if (event.name === "a")
@@ -575,6 +577,31 @@ export function PluginsScreen() {
             await modal.message("Error", `Failed: ${error}`, "error");
         }
     };
+    const handleRemoveDeprecated = async () => {
+        const item = selectableItems[pluginsState.selectedIndex];
+        if (!item || item.kind !== "plugin" || !item.plugin.isOrphaned)
+            return;
+        const plugin = item.plugin;
+        modal.loading(`Removing ${plugin.name}...`);
+        try {
+            // Remove from all scopes — try all to clean up stale references
+            const scopes = ["user", "project", "local"];
+            for (const scope of scopes) {
+                try {
+                    await cliUninstallPlugin(plugin.id, scope, state.projectPath);
+                }
+                catch {
+                    // Ignore errors for scopes where it doesn't exist
+                }
+            }
+            modal.hideModal();
+            fetchData();
+        }
+        catch (error) {
+            modal.hideModal();
+            await modal.message("Error", `Failed to remove: ${error}`, "error");
+        }
+    };
     const handleSaveAsProfile = async () => {
         const settings = await readSettings(state.projectPath);
         const enabledPlugins = settings.enabledPlugins ?? {};

package/src/ui/screens/PluginsScreen.tsx

@@ -238,6 +238,7 @@ export function PluginsScreen() {
 		else if (event.name === "u") handleScopeToggle("user");
 		else if (event.name === "p") handleScopeToggle("project");
 		else if (event.name === "l") handleScopeToggle("local");
+		else if (event.name === "d") handleRemoveDeprecated();
 		else if (event.name === "U") handleUpdate();
 		else if (event.name === "a") handleUpdateAll();
 		else if (event.name === "s") handleSaveAsProfile();
@@ -696,6 +697,30 @@ export function PluginsScreen() {
 		}
 	};
 
+	const handleRemoveDeprecated = async () => {
+		const item = selectableItems[pluginsState.selectedIndex];
+		if (!item || item.kind !== "plugin" || !item.plugin.isOrphaned) return;
+
+		const plugin = item.plugin;
+		modal.loading(`Removing ${plugin.name}...`);
+		try {
+			// Remove from all scopes — try all to clean up stale references
+			const scopes: PluginScope[] = ["user", "project", "local"];
+			for (const scope of scopes) {
+				try {
+					await cliUninstallPlugin(plugin.id, scope, state.projectPath);
+				} catch {
+					// Ignore errors for scopes where it doesn't exist
+				}
+			}
+			modal.hideModal();
+			fetchData();
+		} catch (error) {
+			modal.hideModal();
+			await modal.message("Error", `Failed to remove: ${error}`, "error");
+		}
+	};
+
 	const handleSaveAsProfile = async () => {
 		const settings = await readSettings(state.projectPath);
 		const enabledPlugins = settings.enabledPlugins ?? {};