agent: Allow to explictly disable tools when using enable_all_context_servers (#29414)

Previously, all MCP tools would be completed regardless if they were
disabled/enabled for the profile. This meant that the "Write" profile
was always using all MCP tools, even if you disabled them in the
settings.

Now, when `enable_all_context_servers` is set to `true`, we will enable
all tools from all MCP servers by default but disable the ones that are
explicitly disabled for the profile.

Also fixes an issue where the tools would not show up as enabled when
using `enable_all_context_servers: true`

Release Notes:

- agent: Fix an issue where MCP tools could not be enabled/disabled

crates/agent/src/assistant_configuration/tool_picker.rs

@@ -272,7 +272,7 @@ impl PickerDelegate for ToolPickerDelegate {
                 .get(id.as_ref())
                 .and_then(|preset| preset.tools.get(&tool.name))
                 .copied()
-                .unwrap_or(false),
+                .unwrap_or(self.profile.enable_all_context_servers),
         };
 
         Some(

crates/agent/src/thread_store.rs

@@ -494,6 +494,22 @@ impl ThreadStore {
                     );
                 });
             }
+            // Enable all the tools from all context servers, but disable the ones that are explicitly disabled
+            for (context_server_id, preset) in &profile.context_servers {
+                self.tools.update(cx, |tools, cx| {
+                    tools.disable(
+                        ToolSource::ContextServer {
+                            id: context_server_id.clone().into(),
+                        },
+                        &preset
+                            .tools
+                            .iter()
+                            .filter_map(|(tool, enabled)| (!enabled).then(|| tool.clone()))
+                            .collect::<Vec<_>>(),
+                        cx,
+                    )
+                })
+            }
         } else {
             for (context_server_id, preset) in &profile.context_servers {
                 self.tools.update(cx, |tools, cx| {