Merge pull request #19 from Elnora-AI/chore/phase-3-tool-name-refresh

Refresh MCP tool name references

Author: rjamul-elnora-ai

elnora/commands/protocol.md

@@ -12,17 +12,17 @@ Generate a bioprotocol using the Elnora AI Platform.
 
 1. If a description was provided as an argument, use it. Otherwise, ask the user what protocol they need.
 
-2. Use `elnora_generate_protocol` with the description:
+2. Use `elnora_protocols_generate` with the description:
    - `description`: The user's protocol request (e.g., "HEK 293 cell maintenance protocol with weekly passaging")
 
 3. Present the generated protocol to the user.
 
-4. If the user wants to iterate, find the task that was created and use `elnora_send_message` to continue the conversation.
+4. If the user wants to iterate, find the task that was created and use `elnora_tasks_send` to continue the conversation.
 
 ## Example
 
 User: `/elnora:protocol Standard PCR protocol for BRCA1 exon 11 amplification`
 
-Action: Call `elnora_generate_protocol` with description "Standard PCR protocol for BRCA1 exon 11 amplification"
+Action: Call `elnora_protocols_generate` with description "Standard PCR protocol for BRCA1 exon 11 amplification"
 
 Present the result to the user formatted as markdown.