docs(seqera-ai): align Enterprise Co-Scientist docs for 26.1

platform-enterprise_docs/enterprise-sidebar.json

@@ -222,15 +222,23 @@
     },
      {
       "type": "category",
-      "label": "Seqera AI CLI",
+      "label": "Co-Scientist",
       "link": {"type": "doc", "id": "seqera-ai/index"},
       "collapsed": true,
       "items": [
         "seqera-ai/get-started",
         "seqera-ai/installation",
         "seqera-ai/authentication",
-        "seqera-ai/command-approval",
+        "seqera-ai/usage-and-cost",
+        "seqera-ai/skills",
+        "seqera-ai/modes",
         "seqera-ai/use-cases",
+        "seqera-ai/command-approval",
+        "seqera-ai/skill-claude-code",
+        "seqera-ai/skill-codex",
+        "seqera-ai/skill-github-copilot",
+        "seqera-ai/skill-other-agents",
+        "seqera-ai/nextflow-lsp",
         "seqera-ai/projects"
       ]
     },

platform-enterprise_docs/seqera-ai/authentication.md

@@ -1,21 +1,13 @@
 ---
 title: "Authentication"
-description: "Login, logout, and session management for Seqera AI CLI"
-date: "15 Dec 2025"
-tags: [seqera-ai, cli, authentication, login]
+description: "Login, logout, and session management for Seqera CLI"
+date created: "2025-12-15"
+tags: [seqera-ai, co-scientist, cli, authentication, login]
 ---
 
-:::caution Seqera AI CLI is in beta
-Seqera AI CLI is currently in beta. Features and commands may change as we continue to improve the product.
-:::
+Co-Scientist uses your Seqera Platform account for authentication. This page describes authentication concepts and step-by-step instructions for managing your sessions.
 
-:::note
-Seqera Cloud users receive $20 in free credits to get started with Seqera AI. [Contact us](https://seqera.io/platform/seqera-ai/request-credits/) for additional credits.
-:::
-
-Seqera AI uses your Seqera Platform account for authentication. This page describes authentication concepts and step-by-step instructions for managing your sessions.
-
-## Authenticating Seqera AI
+## Authenticating Co-Scientist
 
 ### Log in
 
@@ -27,10 +19,10 @@ seqera login
 
 This will:
 
-1. Open your default browser to the Seqera login page
-1. Prompt you to sign in with your Seqera Platform credentials
-1. Automatically capture the authentication token
-1. Display a success message in your terminal
+1. Open your default browser to the Seqera login page.
+1. Prompt you to sign in with your Seqera Platform credentials.
+1. Automatically capture the authentication token.
+1. Display a success message in your terminal.
 
    ```
    [Login] Starting Seqera CLI authentication...
@@ -59,7 +51,36 @@ seqera ai
 
 When this environment variable is set, the CLI skips the OAuth login flow and uses the provided token directly.
 
-For Enterprise backend connection settings and development-build examples, see [Install Seqera AI](../enterprise/install-seqera-ai.md#connect-the-cli-to-seqera-ai).
+### Connect to an Enterprise backend
+
+Set the following environment variables before starting `seqera ai`:
+
+| Variable | Purpose | Example value |
+| --- | --- | --- |
+| `SEQERA_AI_BACKEND_URL` | Co-Scientist backend endpoint used by the CLI | `https://ai-api.platform.example.com` |
+| `SEQERA_AUTH_DOMAIN` | OIDC authority base URL. The CLI fetches OpenID configuration from this URL and opens the discovered authorization endpoint in your browser. | `https://platform.example.com/api` |
+| `SEQERA_AUTH_CLI_CLIENT_ID` | OAuth client ID for the Seqera CLI | `seqera_ai_cli` |
+| `TOWER_ACCESS_TOKEN` | Platform personal access token used instead of browser login | `<PLATFORM_ACCESS_TOKEN>` |
+
+Use the OAuth login flow:
+
+```bash
+export SEQERA_AUTH_DOMAIN=https://platform.example.com/api
+export SEQERA_AUTH_CLI_CLIENT_ID=seqera_ai_cli
+export SEQERA_AI_BACKEND_URL=https://ai-api.platform.example.com
+seqera ai
+```
+
+Use a Platform personal access token instead of browser login:
+
+```bash
+export SEQERA_AUTH_DOMAIN=https://platform.example.com/api
+export TOWER_ACCESS_TOKEN=<PLATFORM_ACCESS_TOKEN>
+export SEQERA_AI_BACKEND_URL=https://ai-api.platform.example.com
+seqera ai
+```
+
+Set `SEQERA_AUTH_CLI_CLIENT_ID` only for OAuth deployments that use a non-default CLI client ID. Current CLI builds still require `SEQERA_AUTH_DOMAIN` for Enterprise token-based authentication so the CLI can target the correct Platform authority.
 
 ### Log out
 
@@ -73,7 +94,7 @@ This command revokes your current authentication token and removes locally store
 
 ## Organization management
 
-Seqera AI CLI supports managing your organization selection for billing. Use the `seqera org` command to view and switch organizations.
+The Seqera CLI supports managing your organization selection for billing. Use the `seqera org` command to view and switch organizations.
 
 **View current organization**:
 
@@ -101,16 +122,17 @@ seqera org clear
 
 ## Token refresh
 
-Seqera AI CLI automatically refreshes your authentication token when needed. You are not required to log in again unless:
+The Seqera CLI automatically refreshes your authentication token when needed. You are not required to log in again unless:
 
 - You explicitly log out
 - Your refresh token expires (typically after extended inactivity)
 - Your Seqera Platform account permissions change
 
 ## Learn more
 
-- [Seqera AI CLI](index.md): Seqera AI CLI overview
+- [Seqera CLI](index.md): Seqera CLI overview
 - [Installation](./installation.mdx): Detailed installation instructions
 - [Command approval](./command-approval.md): Control which commands run automatically
-- [Use cases](./use-cases.md): Seqera AI use cases
+- [Use cases](./use-cases.md): Co-Scientist use cases
+- [Usage and cost](./usage-and-cost.md): Co-Scientist usage in Enterprise deployments
 - [Troubleshooting](../troubleshooting_and_faqs/seqera-ai.md): Troubleshoot common errors

platform-enterprise_docs/seqera-ai/command-approval.md

@@ -1,20 +1,16 @@
 ---
 title: "Command approval"
-description: "Control which local commands require user approval in Seqera AI"
-date: "15 Dec 2025"
-tags: [seqera-ai, cli, approval, security]
+description: "Control which local commands require user approval in Co-Scientist"
+date created: "2025-12-15"
+tags: [seqera-ai, co-scientist, cli, approval, security]
 ---
 
-:::caution Seqera AI CLI is in beta
-Seqera AI CLI is currently in beta. Features and commands may change as we continue to improve the product.
-:::
+Co-Scientist can execute local commands and edit files in your environment. This page explains approval modes that control which operations run automatically versus which require your permission, including dangerous commands, workspace boundaries, and best practices.
 
-:::note
-Seqera Cloud users receive $20 in free credits to get started with Seqera AI. [Contact us](https://seqera.io/platform/seqera-ai/request-credits/) for additional credits.
+:::info
+Starting a persistent task with `/goal <task>` switches the session to `full` approval mode automatically so Co-Scientist can continue working without repeated prompts.
 :::
 
-Seqera AI can execute local commands and edit files in your environment. This page explains approval modes that control which operations run automatically versus which require your permission, including dangerous commands, workspace boundaries, and best practices.
-
 ## Approval prompts
 
 When a command requires approval, you will see a prompt similar to:
@@ -38,7 +34,7 @@ You can:
 
 ## Approval modes
 
-Approval modes control which local commands Seqera AI can execute automatically and which require your explicit approval. This provides a balance between convenience and safety when working with local files and commands.
+Approval modes control which local commands Co-Scientist can execute automatically and which require your explicit approval. This provides a balance between convenience and safety when working with local files and commands.
 
 There are three approval modes:
 
@@ -227,8 +223,9 @@ seqera ai
 
 ## Learn more
 
-- [Seqera AI CLI](index.md): Seqera AI CLI overview
+- [Seqera CLI](index.md): Seqera CLI overview
 - [Installation](./installation): Detailed installation instructions
 - [Authentication](./authentication): Log in, log out, and session management
-- [Use cases](./use-cases.md): Seqera AI use cases
+- [Use cases](./use-cases.md): Co-Scientist use cases
+- [Usage and cost](./usage-and-cost.md): Co-Scientist usage in Enterprise deployments
 - [Troubleshooting](../troubleshooting_and_faqs/seqera-ai.md): Troubleshoot common errors

platform-enterprise_docs/seqera-ai/get-started.md

@@ -1,23 +1,15 @@
 ---
 title: "Get started"
 description: "AI-powered assistant for bioinformatics workflows and Seqera Platform"
-date: "2025-12-16"
-tags: [seqera-ai, cli, ai]
+date created: "2026-03-11"
+tags: [seqera-ai, co-scientist, cli, ai]
 ---
 
-:::caution Seqera AI CLI is in beta
-Seqera AI CLI is currently in beta. Features and commands may change as we continue to improve the product.
-:::
-
-:::note
-Seqera Cloud users receive $20 in free credits to get started with Seqera AI. [Contact us](https://seqera.io/platform/seqera-ai/request-credits/) for additional credits.
-:::
-
 ## Get started
 
-To get started with Seqera AI:
+To get started with Co-Scientist:
 
-1. Install the Seqera AI CLI:
+1. Install the Seqera CLI:
 
     ```bash
     npm install -g seqera
@@ -33,32 +25,55 @@ To get started with Seqera AI:
 
     See [Authentication](./authentication.md) for a comprehensive authentication guide.
 
-    If you are testing a development build of the CLI against the hosted production Seqera AI service, see [Install Seqera AI](../enterprise/install-seqera-ai.md#connect-the-cli-to-seqera-ai) for the required environment variables.
+    For Enterprise deployments, set `SEQERA_AI_BACKEND_URL` to your organization's agent backend before you start Co-Scientist. Your administrator should provide this URL; it maps to `global.agentBackendDomain` in the [Co-Scientist install guide](../enterprise/install-seqera-ai.md). See [Authentication](./authentication.md#connect-to-an-enterprise-backend) for the full environment variable reference.
 
-1. Start Seqera AI:
+1. Start Co-Scientist:
 
     ```bash
     seqera ai
     ```
 
-    You can also start with an initial query:
+1. Open the command palette and review the available built-in commands and skills:
 
-    ```bash
-    seqera ai "list my pipelines"
+    ```
+    /help
+    ```
+
+    You can also type `/` to open command autocomplete.
+
+1. Try build mode and plan mode:
+
+    - Press `Shift+Tab` to switch between **build** and **plan**
+    - Check the current mode in the composer footer
+    - Run `/status` if you want a full status readout
+
+    Example plan-mode prompt:
+
+    ```
+    Compare whether I should add FastQC or fastp as the first QC step in this RNA-seq pipeline, including the workflow changes each option would require
+    ```
+
+1. Run your first workflow-focused prompt:
+
+    ```
+    /debug-last-run-on-seqera
     ```
 
-1. Run your first prompt:
+1. Try goal mode for a longer task:
 
     ```
-    /debug
+    /goal update this pipeline for AWS Batch and add nf-tests
     ```
 
-    See [Use cases](./use-cases.md) for a comprehensive list of use cases.
+    See [Use cases](./use-cases.md) for more examples.
 
 ## Learn more
 
 - [Installation](./installation.mdx): Detailed installation instructions
 - [Authentication](./authentication.md): Log in, log out, and session management
+- [Skills](./skills.md): Discover, create, and install skills
+- [Modes](./modes.md): Work in build mode, plan mode, and goal mode
 - [Command approval](./command-approval.md): Control which commands run automatically
-- [Use cases](./use-cases.md): Seqera AI CLI use cases
+- [Use cases](./use-cases.md): Seqera CLI use cases
+- [Usage and cost](./usage-and-cost.md): Co-Scientist usage in Enterprise deployments
 - [Troubleshooting](../troubleshooting_and_faqs/seqera-ai.md): Troubleshoot common errors

platform-enterprise_docs/seqera-ai/index.md

@@ -1,39 +1,48 @@
 ---
-title: "Seqera AI CLI"
+title: "Co-Scientist in the Seqera CLI"
 description: "AI-powered assistant for bioinformatics workflows and Seqera Platform"
-date: "2025-12-15"
-tags: [seqera-ai, cli, ai]
+date created: "2026-03-11"
+last updated: "2026-04-29"
+tags: [seqera-ai, co-scientist, cli, ai]
 ---
 
-:::caution Seqera AI CLI is in beta
-Seqera AI CLI is currently in beta. Features and commands may change as we continue to improve the product.
-:::
+Co-Scientist combines self-service bioinformatics, interactive intelligence, and autonomous execution into one unified experience.
 
-:::note
-Seqera Cloud users receive $20 in free credits to get started with Seqera AI. [Contact us](https://seqera.io/platform/seqera-ai/request-credits/) for additional credits.
-:::
+You can use the Seqera CLI to build, run, and manage bioinformatics workflows in an interactive terminal experience for working with Nextflow pipelines and Seqera Platform.
 
-Seqera AI CLI is an intelligent command-line assistant that helps you build, run, and manage bioinformatics workflows. Powered by advanced AI, it provides an interactive terminal experience for working with Nextflow pipelines and Seqera Platform.
-
-Seqera AI has access to:
+Co-Scientist has access to:
 
 - **Your Seqera Platform workspace**: View and manage workflows, pipelines, and data through your authenticated account
 - **Your local environment**: Execute commands and edit files in your working directory (with configurable approval controls)
 - **AI capabilities**: Natural language understanding, code generation, and intelligent suggestions
 
-## Seqera AI features
+Co-Scientist can load local project context, including instruction files such as `AGENTS.md`, `CLAUDE.md`, and `CONTEXT.md`, project skills, and files under `.seqera/docs` and `.seqera/memory`. Review local context files before starting a session in a repository that contains sensitive instructions or private run history.
+
+## Co-Scientist features
+
+### Skills
+
+Co-Scientist supports reusable skills for common workflows. Backend skills are exposed as slash commands in the `/` command palette and `/help`, and project or user `SKILL.md` files are discovered automatically from standard skill directories.
 
 ### Natural language interface
 
 Interact with Seqera Platform using plain English. Ask questions, launch workflows, and manage pipelines through conversational commands.
 
+### Build and plan modes
+
+Switch between **build** and **plan** modes during an interactive session with `Shift+Tab`. Build mode is the default for execution and file changes, while plan mode is optimized for analysis, implementation planning, and read-only investigation.
+
+### Goal mode
+
+Use `/goal <task>` to set a persistent goal. Co-Scientist will keep working toward that goal across multiple model attempts until it is complete or the goal attempt limit is reached.
+
 ### Workflow management
 
 Launch, monitor, and debug Nextflow workflows directly from your terminal. Get real-time status updates, view logs, and analyze run metrics.
 
 ### Pipeline development
 
-Generate Nextflow configurations, create pipeline schemas, and convert scripts from other workflow languages (WDL, Snakemake) to Nextflow.
+Generate Nextflow configurations, create pipeline schemas, and convert scripts from other workflow languages (WDL, R) to Nextflow.
 
 ### nf-core integration
 
@@ -65,13 +74,21 @@ Full access to Platform capabilities including compute environments, datasets, d
 
 ### Projects
 
-Organize a workspace into projects by applying Seqera Platform labels prefixed with `project_`. Each project scopes the pipelines, datasets, workflow runs, and chat context the AI sees, without needing a separate CRUD surface in Seqera AI.
+Organize a workspace into projects by applying Seqera Platform labels prefixed with `project_`. Each project scopes the pipelines, datasets, workflow runs, and chat context the AI sees — without needing a separate CRUD surface in Co-Scientist.
 
 ## Learn more
 
 - [Installation](./installation.mdx): Detailed installation instructions
 - [Authentication](./authentication.md): Log in, log out, and session management
+- [Skills](./skills.md): Discover, create, and install skills
+- [Modes](./modes.md): Work in build mode, plan mode, and goal mode
 - [Command approval](./command-approval.md): Control which commands run automatically
-- [Use cases](./use-cases.md): Seqera AI CLI use cases
+- [Working with Claude Code](./skill-claude-code.md): Install Co-Scientist as a skill for Claude Code
+- [Working with Codex](./skill-codex.md): Install Co-Scientist as a skill for Codex
+- [Working with GitHub Copilot](./skill-github-copilot.md): Install Co-Scientist as a skill for GitHub Copilot
+- [Working with other coding agents](./skill-other-agents.md): Install Co-Scientist for other coding agents
+- [Code intelligence](./nextflow-lsp.md): Language-server support in Co-Scientist
+- [Use cases](./use-cases.md): Seqera CLI use cases
 - [Projects](./projects.md): Organize workspace resources into projects using Platform labels
+- [Usage and cost](./usage-and-cost.md): Co-Scientist usage in Enterprise deployments
 - [Troubleshooting](../troubleshooting_and_faqs/seqera-ai.md): Troubleshoot common errors