feat(skills): add agent capabilities, file content search, and presigned uploads

elnora/skills/elnora-agent/SKILL.md

@@ -0,0 +1,59 @@
+---
+name: elnora-agent
+description: >
+  This skill should be used when the user asks about "Elnora agent capabilities",
+  "what can the agent do", "agent tools", "web search", "academic search",
+  "PubMed", "ArXiv", "Exa", "Tavily", "Perplexity", "Valyu", "ToolUniverse",
+  "scientific tools", "agent memory", "code execution", "sandbox",
+  "search papers", "search literature", "drug discovery", "protein analysis",
+  "clinical trials", "file operations", "agent skills",
+  or any question about what the Elnora AI Agent can do when you send it a task.
+---
+
+# Elnora Agent Capabilities
+
+The Elnora Agent is a sandboxed Python environment with ~78 core tools + 2,100 ToolUniverse scientific tools. Interact via `elnora_create_task` / `elnora_send_message` — describe what you need in plain language, don't reference internal tool names.
+
+## MCP Tools for Agent Interaction
+
+| Tool | Purpose |
+|------|---------|
+| `elnora_create_task` | Create a task with optional `initial_message` to start generation |
+| `elnora_send_message` | Send follow-up message. 30-120s for complex requests. |
+| `elnora_get_task_messages` | Read agent responses |
+| `elnora_generate_protocol` | Convenience: create task + send message in one call |
+
+## What the Agent Can Do
+
+| Capability | Examples |
+|------------|----------|
+| **Web search** (34 tools) | Real-time search, neural/semantic search, deep research, URL extraction, site crawling. Providers: Tavily, Exa, Valyu, Perplexity |
+| **Academic databases** (12 tools) | PubMed, ArXiv, Semantic Scholar, bioRxiv, Europe PMC, OpenAlex, UniProt, ClinicalTrials.gov, ChEMBL, Wolfram Alpha |
+| **2,100+ scientific tools** (ToolUniverse) | Protein structure (AlphaFold, PDB), genomics (Ensembl, ClinVar), chemistry (PubChem, DrugBank), pathways (KEGG, Reactome), drug safety (OpenFDA), and 21 more categories |
+| **35 domain skills** | Literature review, experimental design, drug discovery workflow, protein engineering, single-cell RNA QC, statistical analysis, scientific writing |
+| **File operations** (11 tools) | Create/read/search files, full-text grep, upload attachments, link files to tasks |
+| **Memory** (9 tools) | Remember facts across tasks, share findings between agents, recall prior context |
+| **Code execution** | Persistent Python REPL with pandas, numpy, biopython. Variables survive across executions. 30s timeout, 1MB output max |
+
+## Good Prompts
+
+**Web research:**
+> "Search for recent CRISPR delivery methods and summarize the top findings"
+
+**Literature review:**
+> "Search PubMed for BRCA1 DNA repair papers from 2024, find the most cited ones"
+
+**Drug target research:**
+> "Search for compounds targeting EGFR, cross-reference with active clinical trials"
+
+**Scientific computation:**
+> "Use ToolUniverse to run AlphaFold on this sequence: MVLSPADKTNVKAAWGKVGA"
+
+**Memory:**
+> "Remember that our lab uses Q5 polymerase for all high-fidelity PCR at 62C"
+
+**File search:**
+> "Search all project files for mentions of 'annealing temperature' and summarize"
+
+**Reference existing files:**
+Use `file_ids` in `elnora_send_message` or `context_file_ids` in `elnora_create_task` to give the agent context about existing protocols.

elnora/skills/elnora-files/SKILL.md

@@ -145,6 +145,17 @@ Get version history for a file. Use this to track how a protocol evolved across
 
 Returns paginated list of versions with timestamps and metadata.
 
+### elnora_get_version_content
+
+Get the content of a specific historical file version. Essential for comparing versions or reviewing past protocol iterations.
+
+| Parameter | Type | Required | Description |
+|-----------|------|----------|-------------|
+| `file_id` | uuid | Yes | File UUID |
+| `version_id` | uuid | Yes | Version UUID |
+
+Get version IDs from `elnora_get_file_versions` first.
+
 ### elnora_create_version
 
 Create a new version of a file with updated content.
@@ -241,3 +252,49 @@ Change a file's visibility level (e.g., promote to organization library).
 ### Reference a file in a task conversation
 
 Use file IDs from `elnora_list_files` as `file_ids` in `elnora_send_message` or `context_file_ids` in `elnora_create_task` to give the AI context about existing protocols or datasets.
+
+## Presigned URL Upload (Large/Binary Files)
+
+For files too large for inline upload (>100KB) or binary files, use the two-step presigned URL flow:
+
+### elnora_initiate_upload
+
+Start a multi-step file upload. Returns a presigned URL for uploading content directly to storage.
+
+| Parameter | Type | Required | Description |
+|-----------|------|----------|-------------|
+| `project_id` | uuid | Yes | Project UUID |
+| `file_name` | string | Yes | Filename (min: 1, max: 255 chars) |
+| `content_type` | string | No | MIME type (default: application/octet-stream) |
+| `file_size_bytes` | integer | Yes | File size in bytes |
+
+Returns a presigned URL and file ID. PUT the file content to the URL, then confirm.
+
+### elnora_confirm_upload
+
+Confirm that a file upload to the presigned URL has completed.
+
+| Parameter | Type | Required | Description |
+|-----------|------|----------|-------------|
+| `file_id` | uuid | Yes | File UUID from `elnora_initiate_upload` |
+
+## Search Inside Files
+
+### elnora_search_file_content
+
+Full-text search inside file bodies. Finds content within protocols and documents, not just metadata.
+
+| Parameter | Type | Required | Default | Description |
+|-----------|------|----------|---------|-------------|
+| `query` | string | Yes | - | Search query (min: 1, max: 1,000 chars) |
+| `page` | integer | No | 1 | Page number |
+| `page_size` | integer | No | 25 | Results per page (max: 100) |
+
+## Token Efficiency
+
+All file tools support optional `compact` and `fields` parameters:
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `compact` | boolean | false | Strip null/empty values (~30-40% token savings) |
+| `fields` | string | all | Comma-separated field names (e.g., "id,name") |

elnora/skills/elnora-platform/SKILL.md

@@ -25,17 +25,27 @@ Auth is handled automatically by the MCP connection:
 
 No manual login required.
 
+## Token Efficiency
+
+All MCP tools support two optional params for reducing token usage:
+
+| Param | Effect |
+|-------|--------|
+| `compact: true` | Strip null/empty values (~30-40% savings). Always use in agent workflows. |
+| `fields: "id,name"` | Return only specified fields. Applied to each item in paginated results. |
+
 ## Routing Table
 
 | Need | Sub-skill | Trigger keywords |
 |------|-----------|------------------|
 | List/get/create/update/archive projects, manage members | `elnora-projects` | project, workspace, create project, members |
 | Create/manage/message tasks, protocol generation | `elnora-tasks` | task, protocol, send message, generate |
 | Browse/read/upload/create/version/fork files | `elnora-files` | file, content, version history, upload, download, fork |
-| Find tasks or files by keyword | `elnora-search` | search, find, query |
+| Find tasks, files, or content by keyword | `elnora-search` | search, find, query, search file content |
 | Manage project folder trees | `elnora-folders` | folder, create folder, move folder |
 | Org management, members, billing, invitations, shared library | `elnora-orgs` | organization, org, billing, invite, library |
 | Auth, API keys, account, health, diagnostics | `elnora-admin` | api key, health, account, feedback, audit, flags |
+| What can the Elnora Agent do? (tools, search, memory) | `elnora-agent` | agent capabilities, agent tools, what can agent do |
 
 ## Organization Context
 

elnora/skills/elnora-search/SKILL.md

@@ -2,7 +2,8 @@
 name: elnora-search
 description: >
   This skill should be used when the user asks to "search tasks", "find a protocol",
-  "search files", "find tasks about", "look up", "query Elnora", "search Elnora",
+  "search files", "search file content", "search inside files", "find tasks about",
+  "look up", "query Elnora", "search Elnora", "full text search",
   or any task involving searching the Elnora Platform for tasks or files by keyword.
 ---
 
@@ -90,13 +91,35 @@ Full-text search scoped to files only.
 
 Same response shape as `elnora_search_all` but only returns file results. Use this when you know you are looking for a document or protocol output.
 
+### elnora_search_file_content
+
+Full-text search inside file bodies (protocols, documents). Unlike `elnora_search_files` which searches metadata, this searches the actual content of files.
+
+| Parameter | Type | Required | Default | Description |
+|-----------|------|----------|---------|-------------|
+| `query` | string | Yes | - | Search query (min: 1, max: 1,000 chars) |
+| `page` | integer | No | 1 | Page number (min: 1) |
+| `page_size` | integer | No | 25 | Results per page (min: 1, max: 100) |
+
+Same response shape as other search tools. Use this to find specific protocol steps, reagent mentions, or methods within generated protocols.
+
+## Token Efficiency
+
+All search tools support optional `compact` and `fields` parameters:
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `compact` | boolean | false | Strip null/empty values (~30-40% token savings) |
+| `fields` | string | all | Comma-separated field names (e.g., "id,name,snippet") |
+
 ## Choosing the Right Search Tool
 
 | Goal | Tool |
 |------|------|
 | Find anything matching a keyword | `elnora_search_all` |
 | Find a conversation about a topic | `elnora_search_tasks` |
-| Find a protocol document by name or content | `elnora_search_files` |
+| Find a protocol document by name | `elnora_search_files` |
+| Find content INSIDE file bodies | `elnora_search_file_content` |
 | Browse all files in a specific project | `elnora_list_files` (not search) |
 | Browse all tasks in a specific project | `elnora_list_tasks` (not search) |