Sync skills and version from elnora-cli v1.3.1

Author: elnora-bot

.claude-plugin/marketplace.json

@@ -6,7 +6,7 @@
     "url": "https://elnora.ai"
   },
   "metadata": {
-    "version": "1.3.0",
+    "version": "1.3.1",
     "description": "AI-powered bioprotocol generation and lab workflow management plugins"
   },
   "plugins": [

elnora/.claude-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "elnora",
-  "version": "1.3.0",
+  "version": "1.3.1",
   "description": "AI-powered bioprotocol generation and lab workflow management. Connect to the Elnora AI Platform to generate, optimize, and manage bioprotocols for wet-lab experiments.",
   "author": {
     "name": "Elnora AI",

elnora/skills/elnora-platform/SKILL.md

@@ -35,6 +35,10 @@ $CLI projects list --compact            # also works for most commands
 | `--profile <name>` | Named profile (default: `default`). Set with `auth login --api-key <KEY> --profile <name>` |
 | `--json` | Force JSON output |
 
+## Updates
+
+On first use in a session, run `elnora update` to check for updates. If an update is available, inform the user and offer to run `elnora update --install`.
+
 ## Auth
 
 Requires `ELNORA_API_KEY` environment variable (prefix: `elnora_live_`), `ELNORA_MCP_API_KEY`, or a saved profile in `~/.elnora/profiles.toml`.
@@ -136,13 +140,15 @@ HTTP 429 on limit. Check the `Retry-After` header for seconds to wait.
 
 Projects contain tasks and files. Typical flow:
 
-1. `projects list` -> get project ID
+1. `--compact --fields "id,name" projects list` -> list projects, pick one by name
 2. `tasks create --project <ID> --message "..." --stream` -> create task and stream the agent response
 3. `tasks send <TASK_ID> --message "..." --stream` -> send follow-up and stream response
 4. `tasks messages <TASK_ID>` -> read conversation history (or use `--wait` instead of `--stream` in steps 2-3)
 5. `files list --project <ID>` -> browse generated outputs
 6. `files content <FILE_ID>` -> read a protocol file
 
+**Project ID:** List projects once (step 1), pick the one matching the user's context, and reuse the ID for all subsequent commands. Don't re-list projects for every task.
+
 See `elnora-tasks` skill for full response retrieval details (`--stream`, `--wait`, MCP behavior).
 
 ## All Command Groups
@@ -167,6 +173,6 @@ elnora projects     Manage projects
 elnora search       Search tasks, files, and file content
 elnora setup        Configure AI coding tools (Claude Code, Cursor, VS Code, Codex)
 elnora tasks        Manage tasks
-elnora update       Self-update the CLI to the latest version
+elnora update       Check for updates (use --install to apply)
 elnora whoami       Show current profile and org
 ```

elnora/skills/elnora-projects/SKILL.md

@@ -112,10 +112,12 @@ Removes the current user from the project.
 
 ## Agent Recipes
 
-**Get the default project ID:**
+**List projects and pick one:**
 
 ```bash
-$CLI --compact --fields "id,name" projects list --page-size 5
+$CLI --compact --fields "id,name" projects list
+# Pick the project matching the user's context by name. If only one project, use it.
+# If multiple and unclear, ask the user which project to use.
 ```
 
 **Full project setup with members:**

elnora/skills/elnora-tasks/SKILL.md

@@ -40,6 +40,17 @@ SSE event types:
 
 **IMPORTANT — Always show the full response:** When Elnora returns a response (protocol, literature review, analysis, etc.), print the **entire** assistant content back to the user. No truncation, no summarization, no "here are the key points." The user asked Elnora to generate something — show them everything Elnora said, including comments, suggestions, warnings, and explanations. Strip JSON wrapper/metadata but preserve all human-readable content.
 
+## Getting a Project ID
+
+Every task belongs to a project. You need a project ID to create tasks. **Do this once per session, then reuse the ID.**
+
+```bash
+# List the user's projects
+elnora --compact --fields "id,name" projects list
+```
+
+Pick the project that best matches the user's request by name. If there's only one project, use it. If unsure, ask the user which project to use. **Remember the project ID** — don't re-list projects for every task command.
+
 ## Invocation
 
 ```bash
@@ -165,38 +176,27 @@ MCP tools accept the same parameters as CLI flags (camelCase). `elnora_tasks_sen
 
 ## Agent Recipes
 
-**Create task and stream the response:**
+**Typical workflow (list projects → create task → stream response):**
 
 ```bash
-PROJECT=$($CLI --compact --fields "id" projects list | jq -r '.items[0].id')
+# Step 1: Get the project ID (do this once, reuse for all commands)
+$CLI --compact --fields "id,name" projects list
+# Pick the project that matches the user's context. Example with one project:
+# PROJECT="bfdc6fbd-40ed-4042-9ea7-c79a5ec90085"
+
+# Step 2: Create task and stream
 $CLI --compact tasks create --project "$PROJECT" --title "PCR BRCA1" --message "Generate PCR protocol for BRCA1 exon 11" --stream
 ```
 
-**Two-step (capture task ID, then stream follow-ups):**
+**Continue a conversation (reuse task ID):**
 
 ```bash
-TASK=$($CLI --compact tasks create --project "$PROJECT" --title "PCR BRCA1" | jq -r '.id')
-$CLI --compact tasks send "$TASK" --message "Generate PCR protocol for BRCA1 exon 11" --stream
 $CLI --compact tasks send "$TASK" --message "Add gel electrophoresis step" --stream
-```
-
-**Get response as JSON (--wait):**
-
-```bash
-$CLI --compact tasks send "$TASK" --message "Add gel electrophoresis step" --wait
+$CLI --compact tasks send "$TASK" --message "Reduce annealing temperature to 55C" --stream
 ```
 
 **Read conversation history:**
 
 ```bash
 $CLI --compact tasks messages <TASK_ID> | jq '.items[-1] | select(.role == "assistant") | .content'
 ```
-
-**Manual polling fallback (custom timeout):**
-
-```bash
-LAST=$($CLI --compact tasks messages <TASK_ID> | jq '.items[-1]')
-echo "$LAST" | jq '{role: .role, status: (.metadata | fromjson? // {} | .status)}'
-# -> {"role":"assistant","status":"completed"}  <- ready
-# -> {"role":"user","status":null}              <- still processing
-```