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

clear() previously removed all non-manual elements, which destroyed
dynamically registered tools when setDiscoveryState() was called on
the next request cycle. Add isDiscovered flag to ElementReference so
clear() only removes elements that were imported via setDiscoveryState(),
preserving both manual and dynamic registrations.

Author: soyuka

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)"
     }
   ]
 }