fix: clear() wiping dynamically registered tools by tracking discovered state on references

src/Capability/Registry.php

@@ -161,36 +161,10 @@ public function registerPrompt(
 
     public function clear(): void
     {
-        $clearCount = 0;
-
-        foreach ($this->tools as $name => $tool) {
-            if (!$tool->isManual) {
-                unset($this->tools[$name]);
-                ++$clearCount;
-            }
-        }
-        foreach ($this->resources as $uri => $resource) {
-            if (!$resource->isManual) {
-                unset($this->resources[$uri]);
-                ++$clearCount;
-            }
-        }
-        foreach ($this->prompts as $name => $prompt) {
-            if (!$prompt->isManual) {
-                unset($this->prompts[$name]);
-                ++$clearCount;
-            }
-        }
-        foreach ($this->resourceTemplates as $uriTemplate => $template) {
-            if (!$template->isManual) {
-                unset($this->resourceTemplates[$uriTemplate]);
-                ++$clearCount;
-            }
-        }
-
-        if ($clearCount > 0) {
-            $this->logger->debug(\sprintf('Removed %d discovered elements from internal registry.', $clearCount));
-        }
+        $this->tools = array_filter($this->tools, static fn ($t) => !$t->isDiscovered);
+        $this->resources = array_filter($this->resources, static fn ($r) => !$r->isDiscovered);
+        $this->prompts = array_filter($this->prompts, static fn ($p) => !$p->isDiscovered);
+        $this->resourceTemplates = array_filter($this->resourceTemplates, static fn ($t) => !$t->isDiscovered);
     }
 
     public function hasTools(): bool
@@ -344,10 +318,10 @@ public function getPrompt(string $name): PromptReference
     public function getDiscoveryState(): DiscoveryState
     {
         return new DiscoveryState(
-            tools: array_filter($this->tools, static fn ($tool) => !$tool->isManual),
-            resources: array_filter($this->resources, static fn ($resource) => !$resource->isManual),
-            prompts: array_filter($this->prompts, static fn ($prompt) => !$prompt->isManual),
-            resourceTemplates: array_filter($this->resourceTemplates, static fn ($template) => !$template->isManual),
+            tools: array_filter($this->tools, static fn ($t) => $t->isDiscovered),
+            resources: array_filter($this->resources, static fn ($r) => $r->isDiscovered),
+            prompts: array_filter($this->prompts, static fn ($p) => $p->isDiscovered),
+            resourceTemplates: array_filter($this->resourceTemplates, static fn ($t) => $t->isDiscovered),
         );
     }
 
@@ -360,21 +334,29 @@ public function setDiscoveryState(DiscoveryState $state): void
         // Clear existing discovered elements
         $this->clear();
 
-        // Import new discovered elements
+        // Import new discovered elements — skip any that conflict with manual or dynamic registrations
         foreach ($state->getTools() as $name => $tool) {
-            $this->tools[$name] = $tool;
+            if (!isset($this->tools[$name])) {
+                $this->tools[$name] = new ToolReference($tool->tool, $tool->handler, isDiscovered: true);
+            }
         }
 
         foreach ($state->getResources() as $uri => $resource) {
-            $this->resources[$uri] = $resource;
+            if (!isset($this->resources[$uri])) {
+                $this->resources[$uri] = new ResourceReference($resource->resource, $resource->handler, isDiscovered: true);
+            }
         }
 
         foreach ($state->getPrompts() as $name => $prompt) {
-            $this->prompts[$name] = $prompt;
+            if (!isset($this->prompts[$name])) {
+                $this->prompts[$name] = new PromptReference($prompt->prompt, $prompt->handler, completionProviders: $prompt->completionProviders, isDiscovered: true);
+            }
         }
 
         foreach ($state->getResourceTemplates() as $uriTemplate => $template) {
-            $this->resourceTemplates[$uriTemplate] = $template;
+            if (!isset($this->resourceTemplates[$uriTemplate])) {
+                $this->resourceTemplates[$uriTemplate] = new ResourceTemplateReference($template->resourceTemplate, $template->handler, completionProviders: $template->completionProviders, isDiscovered: true);
+            }
         }
 
         // Dispatch events for the imported elements

src/Capability/Registry/ElementReference.php

@@ -24,6 +24,7 @@ class ElementReference
     public function __construct(
         public readonly \Closure|array|string $handler,
         public readonly bool $isManual = false,
+        public readonly bool $isDiscovered = false,
     ) {
     }
 }

src/Capability/Registry/PromptReference.php

@@ -31,8 +31,9 @@ public function __construct(
         \Closure|array|string $handler,
         bool $isManual = false,
         public readonly array $completionProviders = [],
+        bool $isDiscovered = false,
     ) {
-        parent::__construct($handler, $isManual);
+        parent::__construct($handler, $isManual, $isDiscovered);
     }
 
     /**

src/Capability/Registry/ResourceReference.php

@@ -29,8 +29,9 @@ public function __construct(
         public readonly Resource $resource,
         callable|array|string $handler,
         bool $isManual = false,
+        bool $isDiscovered = false,
     ) {
-        parent::__construct($handler, $isManual);
+        parent::__construct($handler, $isManual, $isDiscovered);
     }
 
     /**

src/Capability/Registry/ResourceTemplateReference.php

@@ -38,8 +38,9 @@ public function __construct(
         callable|array|string $handler,
         bool $isManual = false,
         public readonly array $completionProviders = [],
+        bool $isDiscovered = false,
     ) {
-        parent::__construct($handler, $isManual);
+        parent::__construct($handler, $isManual, $isDiscovered);
 
         $this->compileTemplate();
     }

src/Capability/Registry/ToolReference.php

@@ -29,8 +29,9 @@ public function __construct(
         public readonly Tool $tool,
         callable|array|string $handler,
         bool $isManual = false,
+        bool $isDiscovered = false,
     ) {
-        parent::__construct($handler, $isManual);
+        parent::__construct($handler, $isManual, $isDiscovered);
     }
 
     /**

tests/Inspector/Http/snapshots/HttpCombinedRegistrationTest-resources_list.json

@@ -1,9 +1,9 @@
 {
   "resources": [
     {
-      "name": "priority_config_discovered",
+      "name": "priority_config_manual",
       "uri": "config://priority",
-      "description": "A resource discovered via attributes.\n\nThis will be overridden by a manual registration with the same URI."
+      "description": "Manually registered resource that overrides a discovered one."
     }
   ]
 }

tests/Inspector/Http/snapshots/HttpCombinedRegistrationTest-resources_read-config_priority.json

@@ -3,7 +3,7 @@
     {
       "uri": "config://priority",
       "mimeType": "text/plain",
-      "text": "Discovered Priority Config: Low"
+      "text": "Manual Priority Config: HIGH (overrides discovered)"
     }
   ]
 }