clean up approach by moving cleantools inside builder, this simplifie…

…s remote server too
SamMorrowDrums · Jan 15, 2026 · Jan 9, 2026 · Jan 9, 2026 · Jan 9, 2026 · Jan 12, 2026
commit bf9d3821a3b824a6def540348f1e34ec787763ed
@@ -221,7 +221,7 @@ func NewMCPServer(cfg MCPServerConfig) (*mcp.Server, error) {
 		WithDeprecatedAliases(github.DeprecatedToolAliases).
 		WithReadOnly(cfg.ReadOnly).
 		WithToolsets(enabledToolsets).
-		WithTools(github.CleanTools(cfg.EnabledTools)).
+		WithTools(cfg.EnabledTools).
 		WithFeatureChecker(createFeatureChecker(cfg.EnabledFeatures))
 
 	// Apply token scope filtering if scopes are known (for PAT filtering)

@@ -101,6 +101,7 @@ func (b *Builder) WithToolsets(toolsetIDs []string) *Builder {
 // WithTools specifies additional tools that bypass toolset filtering.
 // These tools are additive - they will be included even if their toolset is not enabled.
 // Read-only filtering still applies to these tools.
+// Input is cleaned (trimmed, deduplicated) during Build().
 // Deprecated tool aliases are automatically resolved to their canonical names during Build().
 // Returns self for chaining.
 func (b *Builder) WithTools(toolNames []string) *Builder {
@@ -127,6 +128,24 @@ func (b *Builder) WithFilter(filter ToolFilter) *Builder {
 	return b
 }
 
+// cleanTools trims whitespace and removes duplicates from tool names.
+// Empty strings after trimming are excluded.
+func cleanTools(tools []string) []string {
+	seen := make(map[string]bool)
+	var cleaned []string
+	for _, name := range tools {
+		trimmed := strings.TrimSpace(name)
+		if trimmed == "" {
+			continue
+		}
+		if !seen[trimmed] {
+			seen[trimmed] = true
+			cleaned = append(cleaned, trimmed)
+		}
+	}
+	return cleaned
+}
+
 // Build creates the final Inventory with all configuration applied.
 // This processes toolset filtering, tool name resolution, and sets up
 // the inventory for use. The returned Inventory is ready for use with
@@ -151,12 +170,13 @@ func (b *Builder) Build() *Inventory {
 		validToolNames[b.tools[i].Tool.Name] = true
 	}
 
-	// Process additional tools (resolve aliases and track unrecognized)
-	// Note: input is expected to be pre-cleaned (trimmed, deduped) via CleanTools
+	// Process additional tools (clean, resolve aliases, and track unrecognized)
 	if len(b.additionalTools) > 0 {
-		r.additionalTools = make(map[string]bool, len(b.additionalTools))
+		cleanedTools := cleanTools(b.additionalTools)
+
+		r.additionalTools = make(map[string]bool, len(cleanedTools))
 		var unrecognizedTools []string
-		for _, name := range b.additionalTools {
+		for _, name := range cleanedTools {
 			// Always include the original name - this handles the case where
 			// the tool exists but is controlled by a feature flag that's OFF.
 			r.additionalTools[name] = true