seqeralabs · llewellyn-sl · Mar 12, 2026 · Mar 11, 2026 · Mar 11, 2026 · Mar 11, 2026
diff --git a/platform-cloud/cloud-sidebar.json b/platform-cloud/cloud-sidebar.json
@@ -169,6 +169,8 @@
         "seqera-ai/get-started",
         "seqera-ai/installation",
         "seqera-ai/authentication",
+        "seqera-ai/skills",
+        "seqera-ai/modes",
         "seqera-ai/use-cases",
         "seqera-ai/command-approval",
         "seqera-ai/skill-claude-code",

diff --git a/platform-cloud/docs/seqera-ai/authentication.md b/platform-cloud/docs/seqera-ai/authentication.md
@@ -1,7 +1,7 @@
 ---
 title: "Authentication"
 description: "Login, logout, and session management for Seqera AI CLI"
-date: "15 Dec 2025"
+date created: "2025-12-15"
 tags: [seqera-ai, cli, authentication, login]
 ---
 

diff --git a/platform-cloud/docs/seqera-ai/command-approval.md b/platform-cloud/docs/seqera-ai/command-approval.md
@@ -1,7 +1,7 @@
 ---
 title: "Command approval"
 description: "Control which local commands require user approval in Seqera AI"
-date: "15 Dec 2025"
+date created: "2025-12-15"
 tags: [seqera-ai, cli, approval, security]
 ---
 
@@ -11,6 +11,10 @@ Seqera Cloud users receive $20 in free credits to get started with Seqera AI. [C
 
 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.
 
+:::info
+Starting a persistent task with `/goal <task>` switches the session to `full` approval mode automatically so Seqera AI can continue working without repeated prompts.
+:::
+
 ## Approval prompts
 
 When a command requires approval, you will see output similar to:

diff --git a/platform-cloud/docs/seqera-ai/get-started.md b/platform-cloud/docs/seqera-ai/get-started.md
@@ -1,7 +1,7 @@
 ---
 title: "Get started"
 description: "AI-powered assistant for bioinformatics workflows and Seqera Platform"
-date: "2025-12-16"
+date created: "2026-03-11"
 tags: [seqera-ai, cli, ai]
 ---
 
@@ -36,18 +36,46 @@ To get started with Seqera AI:
     seqera ai
     ```
 
-1. Run your first prompt:
+1. Open the command palette and review the available built-in commands and skills:
+
+    ```
+    /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
     ```
 
-    See [Use cases](./use-cases.md) for a comprehensive list of use cases.
+1. Try goal mode for a longer task:
+
+    ```
+    /goal update this pipeline for AWS Batch and add nf-tests
+    ```
+
+    See [Use cases](./use-cases.md) for more examples.
 
 ## Learn more
 
 - [Installation](./installation.md): 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
 - [Troubleshooting](../troubleshooting_and_faqs/seqera-ai.md): Troubleshoot common errors
diff --git a/platform-cloud/docs/seqera-ai/index.md b/platform-cloud/docs/seqera-ai/index.md
@@ -1,7 +1,7 @@
 ---
 title: "Seqera AI CLI"
 description: "AI-powered assistant for bioinformatics workflows and Seqera Platform"
-date: "2025-12-15"
+date created: "2026-03-11"
 tags: [seqera-ai, cli, ai]
 ---
 
@@ -19,10 +19,22 @@ Seqera AI has access to:
 
 ## Seqera AI features
 
+### Skills
+
+Seqera AI 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. Seqera AI 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.
@@ -55,6 +67,8 @@ Full access to Platform capabilities including compute environments, datasets, d
 
 - [Installation](./installation.md): 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
 - [Working with Claude Code](./skill-claude-code.md): Install Seqera AI as a skill for Claude Code
 - [Working with Codex](./skill-codex.md): Install Seqera AI as a skill for Codex

diff --git a/platform-cloud/docs/seqera-ai/installation.md b/platform-cloud/docs/seqera-ai/installation.md
@@ -1,7 +1,7 @@
 ---
 title: "Installation"
 description: "Install and configure Seqera AI CLI"
-date: "15 Dec 2025"
+date created: "2026-03-11"
 tags: [seqera-ai, cli, installation]
 ---
 
@@ -34,6 +34,26 @@ seqera --version
 npm update -g seqera
 ```
 
+### Install agent integrations
+
+Install Seqera AI as a skill for your coding agent:
+
+```bash
+seqera skill install
+```
+
+Install directly into the current repository:
+
+```bash
+seqera skill install --local
+```
+
+Check installed skills and update them after upgrading the CLI:
+
+```bash
+seqera skill check --update
+```
+
 :::info
 If you use Seqera AI as a skill for a coding agent, run `seqera skill check --update` after updating the CLI to keep your installed skills in sync with the current version. By default, this scans both local and global installations. Use `--global` or `--local` to narrow the scope. See [Working with Claude Code](./skill-claude-code.md), [Working with Codex](./skill-codex.md), [Working with GitHub Copilot](./skill-github-copilot.md), and [Working with other coding agents](./skill-other-agents.md).
 
@@ -52,6 +72,8 @@ npm uninstall -g seqera
 
 - [Seqera AI CLI](index.md): Seqera AI CLI overview
 - [Authentication](./authentication.md): Login, logout, 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
 - [Troubleshooting](../troubleshooting_and_faqs/seqera-ai.md): Troubleshoot common errors
diff --git a/platform-cloud/docs/seqera-ai/modes.md b/platform-cloud/docs/seqera-ai/modes.md
@@ -0,0 +1,115 @@
+---
+title: "Modes"
+description: "Work in build mode, plan mode, and goal mode in Seqera AI CLI"
+date created: "2026-03-11"
+tags: [seqera-ai, cli, modes]
+---
+
+:::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 includes **build mode**, **plan mode**, and **goal mode** so you can choose the right level of autonomy for each task.
+
+## Build mode
+
+Build mode is the default interactive mode. Seqera AI can:
+
+- Read and search files
+- Execute commands
+- Edit or create files
+- Carry out workflow changes directly in your workspace
+
+Use build mode for implementation work, debugging, code generation, and file edits.
+
+## Plan mode
+
+Plan mode is optimized for analysis and implementation planning.
+
+In plan mode, Seqera AI focuses on:
+
+- Understanding the problem
+- Comparing approaches and trade-offs
+- Producing a step-by-step implementation plan
+- Reading files and searching code for context
+
+Plan mode blocks write and execution tools, including:
+
+- `execute_bash_local`
+- `write_file_local`
+- `edit_file_local`
+- `create_directory_local`
+
+If the assistant tries to use one of these tools, the request is rejected and the assistant is told to switch back to build mode.
+
+## Switch between build mode and plan mode
+
+Toggle modes during a session with `Shift+Tab`.
+
+You can also:
+
+- Check the current mode in the composer footer
+- Run `/status` to view the current mode alongside session and LSP status
+- Use `/help` to see mode-aware command guidance
+
+## Goal mode
+
+Goal mode is a persistent workflow for longer tasks. Set a goal with:
+
+```bash
+/goal <task description>
+```
+
+When goal mode is active, Seqera AI:
+
+- Keeps working toward the same objective over multiple model attempts
+- Automatically continues if more work is needed
+- Stops when the goal is complete or the goal attempt limit is reached
+- Switches approval mode to `full` so work can continue without repeated prompts
+
+Goal mode commands:
+
+```bash
+/goal
+/goal off
+```
+
+Run `/goal` without arguments to inspect the current goal. Run `/goal off` to disable goal mode.
+
+Seqera AI currently gives goal mode up to **3 model attempts** before it stops and asks you to start a new goal.
+
+## Keyboard shortcuts
+
+| Shortcut | Action |
+|----------|--------|
+| `Shift+Tab` | Toggle between build mode and plan mode |
+| `Ctrl+Enter` | If your terminal supports it, interrupt the current response and send a queued follow-up immediately |
+| `Esc` | Clear a queued follow-up or interrupt the current response |
+
+## Examples
+
+### Plan mode
+
+```text
+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
+```
+
+```text
+Inspect this repository and outline the changes needed for Seqera Platform deployment
+```
+
+### Goal mode
+
+```text
+/goal migrate this pipeline to DSL2 and add nf-tests
+```
+
+```text
+/goal update this workflow for AWS Batch and verify the config
+```
+
+## Learn more
+
+- [Skills](./skills.md): Discover, create, and install skills
+- [Command approval](./command-approval.md): Control which commands run automatically
+- [Use cases](./use-cases.md): Seqera AI CLI use cases
diff --git a/platform-cloud/docs/seqera-ai/nextflow-lsp.md b/platform-cloud/docs/seqera-ai/nextflow-lsp.md
@@ -1,7 +1,7 @@
 ---
 title: "Language server"
 description: "Use language-server code intelligence features in Seqera AI"
-date: "2026-02-26"
+date created: "2026-02-26"
 tags: [seqera-ai, cli, lsp, code-intelligence]
 ---
 

diff --git a/platform-cloud/docs/seqera-ai/skill-claude-code.md b/platform-cloud/docs/seqera-ai/skill-claude-code.md
@@ -1,7 +1,7 @@
 ---
 title: "Working with Claude Code"
 description: "Install and maintain the Seqera AI skill for Claude Code"
-date: "2026-02-26"
+date created: "2026-03-11"
 tags: [seqera-ai, cli, skills, claude-code]
 ---
 
@@ -13,12 +13,24 @@ The `seqera skill` command installs a skill file that enables [Claude Code](http
 
 ### `seqera skill install`
 
+Launch the interactive installer:
+
+```bash
+seqera skill install
+```
+
 Install to the standard Claude Code location:
 
 ```bash
 seqera skill install --path .claude/skills/
 ```
 
+Install into the current repository root:
+
+```bash
+seqera skill install --local
+```
+
 Or install to your home directory:
 
 ```bash
@@ -41,6 +53,7 @@ seqera skill install [OPTIONS]
 
 | Option | Short | Description |
 |--------|-------|-------------|
+| `--local` | `-l` | Install to repo root |
 | `--path <PATH>` | `-p` | Install to a custom path (relative or absolute) |
 | `--global` | `-g` | Install to home directory |
 | `--detect` | `-d` | Auto-detect an existing installation and update it |
@@ -75,6 +88,7 @@ seqera skill check [OPTIONS]
 
 ### Learn more
 
+- [Skills](./skills.md): Discover, create, and install skills
 - [Use cases](./use-cases.md): Seqera AI CLI use cases
 - [Code intelligence](./nextflow-lsp.md): Language-aware coding support
 - [Installation](./installation.md): Detailed installation instructions