fixed flaky tests & /tools

Author: jrobertboos

tests/e2e/features/skills.feature

@@ -12,6 +12,7 @@ Feature: Agent skills tests
   @SkillsConfig @skip
   Scenario: Skill tools are registered when skills are configured
     Given The service uses the lightspeed-stack-skills.yaml configuration
+      And MCP toolgroups are reset for a new MCP configuration
       And The service is restarted
     When I access REST API endpoint "tools" using HTTP GET method
     Then The status code of the response is 200
@@ -132,6 +133,7 @@ Feature: Agent skills tests
 
   Scenario: Skill tools are not registered when no skills are configured
     Given The service uses the lightspeed-stack.yaml configuration
+      And MCP toolgroups are reset for a new MCP configuration
       And The service is restarted
     When I access REST API endpoint "tools" using HTTP GET method
     Then The status code of the response is 200
@@ -644,7 +646,7 @@ Feature: Agent skills tests
 
   # --- Full progressive disclosure flow ---
 
-  @SkillsConfig
+  @SkillsConfig @flaky
   Scenario: LLM completes list_skills then load_skill then read_skill_resource via query endpoint
     Given The service uses the lightspeed-stack-skills.yaml configuration
       And The service is restarted
@@ -703,7 +705,7 @@ Feature: Agent skills tests
       """
 
 
-  @SkillsConfig
+  @SkillsConfig @flaky
   Scenario: LLM completes list_skills then load_skill then read_skill_resource via streaming_query endpoint
     Given The service uses the lightspeed-stack-skills.yaml configuration
       And The service is restarted