More doc changes

docs/modules/usage/configuration-options.md

@@ -7,53 +7,11 @@ If you are running in [GUI Mode](https://docs.all-hands.dev/modules/usage/how-to
 take precedence.
 :::
 
----
-
-# Table of Contents
-
-- [Core Configuration](#core-configuration)
-   - [API Keys](#api-keys)
-   - [Workspace](#workspace)
-   - [Debugging and Logging](#debugging-and-logging)
-   - [Session Management](#session-management)
-   - [Trajectories](#trajectories)
-   - [File Store](#file-store)
-   - [Task Management](#task-management)
-   - [Sandbox Configuration](#sandbox-configuration)
-   - [Miscellaneous](#miscellaneous)
-- [LLM Configuration](#llm-configuration)
-   - [AWS Credentials](#aws-credentials)
-   - [API Configuration](#api-configuration)
-   - [Custom LLM Provider](#custom-llm-provider)
-   - [Embeddings](#embeddings)
-   - [Message Handling](#message-handling)
-   - [Model Selection](#model-selection)
-   - [Retrying](#retrying)
-   - [Advanced Options](#advanced-options)
-- [Agent Configuration](#agent-configuration)
-   - [Microagent Configuration](#microagent-configuration)
-   - [Memory Configuration](#memory-configuration)
-   - [LLM Configuration](#llm-configuration-2)
-   - [ActionSpace Configuration](#actionspace-configuration)
-   - [Microagent Usage](#microagent-usage)
-- [Sandbox Configuration](#sandbox-configuration)
-   - [Execution](#execution)
-   - [Container Image](#container-image)
-   - [Networking](#networking)
-   - [Linting and Plugins](#linting-and-plugins)
-   - [Dependencies and Environment](#dependencies-and-environment)
-   - [Evaluation](#evaluation)
-- [Security Configuration](#security-configuration)
-   - [Confirmation Mode](#confirmation-mode)
-   - [Security Analyzer](#security-analyzer)
-
----
-
 ## Core Configuration
 
 The core configuration options are defined in the `[core]` section of the `config.toml` file.
 
-**API Keys**
+### API Keys
 - `e2b_api_key`
   - Type: `str`
   - Default: `""`
@@ -69,7 +27,7 @@ The core configuration options are defined in the `[core]` section of the `confi
   - Default: `""`
   - Description: API token secret for Modal
 
-**Workspace**
+### Workspace
 - `workspace_base`
   - Type: `str`
   - Default: `"./workspace"`
@@ -80,7 +38,7 @@ The core configuration options are defined in the `[core]` section of the `confi
   - Default: `"/tmp/cache"`
   - Description: Cache directory path
 
-**Debugging and Logging**
+### Debugging and Logging
 - `debug`
   - Type: `bool`
   - Default: `false`
@@ -91,13 +49,13 @@ The core configuration options are defined in the `[core]` section of the `confi
   - Default: `false`
   - Description: Disable color in terminal output
 
-**Trajectories**
+### Trajectories
 - `trajectories_path`
   - Type: `str`
   - Default: `"./trajectories"`
   - Description: Path to store trajectories (can be a folder or a file). If it's a folder, the trajectories will be saved in a file named with the session id name and .json extension, in that folder.
 
-**File Store**
+### File Store
 - `file_store_path`
   - Type: `str`
   - Default: `"/tmp/file_store"`
@@ -128,7 +86,7 @@ The core configuration options are defined in the `[core]` section of the `confi
   - Default: `[".*"]`
   - Description: List of allowed file extensions for uploads
 
-**Task Management**
+### Task Management
 - `max_budget_per_task`
   - Type: `float`
   - Default: `0.0`
@@ -139,7 +97,7 @@ The core configuration options are defined in the `[core]` section of the `confi
   - Default: `100`
   - Description: Maximum number of iterations
 
-**Sandbox Configuration**
+### Sandbox Configuration
 - `workspace_mount_path_in_sandbox`
   - Type: `str`
   - Default: `"/workspace"`
@@ -155,7 +113,7 @@ The core configuration options are defined in the `[core]` section of the `confi
   - Default: `""`
   - Description: Path to rewrite the workspace mount path to. You can usually ignore this, it refers to special cases of running inside another container.
 
-**Miscellaneous**
+### Miscellaneous
 - `run_as_openhands`
   - Type: `bool`
   - Default: `true`
@@ -182,7 +140,7 @@ The LLM (Large Language Model) configuration options are defined in the `[llm]`
 
 To use these with the docker command, pass in `-e LLM_<option>`. Example: `-e LLM_NUM_RETRIES`.
 
-**AWS Credentials**
+### AWS Credentials
 - `aws_access_key_id`
   - Type: `str`
   - Default: `""`
@@ -198,7 +156,7 @@ To use these with the docker command, pass in `-e LLM_<option>`. Example: `-e LL
   - Default: `""`
   - Description: AWS secret access key
 
-**API Configuration**
+### API Configuration
 - `api_key`
   - Type: `str`
   - Default: `None`
@@ -224,13 +182,13 @@ To use these with the docker command, pass in `-e LLM_<option>`. Example: `-e LL
   - Default: `0.0`
   - Description: Cost per output token
 
-**Custom LLM Provider**
+### Custom LLM Provider
 - `custom_llm_provider`
   - Type: `str`
   - Default: `""`
   - Description: Custom LLM provider
 
-**Embeddings**
+### Embeddings
 - `embedding_base_url`
   - Type: `str`
   - Default: `""`
@@ -246,7 +204,7 @@ To use these with the docker command, pass in `-e LLM_<option>`. Example: `-e LL
   - Default: `"local"`
   - Description: Embedding model to use
 
-**Message Handling**
+### Message Handling
 - `max_message_chars`
   - Type: `int`
   - Default: `30000`
@@ -262,13 +220,13 @@ To use these with the docker command, pass in `-e LLM_<option>`. Example: `-e LL
   - Default: `0`
   - Description: Maximum number of output tokens
 
-**Model Selection**
+### Model Selection
 - `model`
   - Type: `str`
   - Default: `"claude-3-5-sonnet-20241022"`
   - Description: Model to use
 
-**Retrying**
+### Retrying
 - `num_retries`
   - Type: `int`
   - Default: `8`
@@ -289,7 +247,7 @@ To use these with the docker command, pass in `-e LLM_<option>`. Example: `-e LL
   - Default: `2.0`
   - Description: Multiplier for exponential backoff calculation
 
-**Advanced Options**
+### Advanced Options
 - `drop_params`
   - Type: `bool`
   - Default: `false`
@@ -329,13 +287,13 @@ To use these with the docker command, pass in `-e LLM_<option>`. Example: `-e LL
 
 The agent configuration options are defined in the `[agent]` and `[agent.<agent_name>]` sections of the `config.toml` file.
 
-**Microagent Configuration**
+### Microagent Configuration
 - `micro_agent_name`
   - Type: `str`
   - Default: `""`
   - Description: Name of the micro agent to use for this agent
 
-**Memory Configuration**
+### Memory Configuration
 - `memory_enabled`
   - Type: `bool`
   - Default: `false`
@@ -346,13 +304,13 @@ The agent configuration options are defined in the `[agent]` and `[agent.<agent_
   - Default: `3`
   - Description: The maximum number of threads indexing at the same time for embeddings
 
-**LLM Configuration**
+### LLM Configuration
 - `llm_config`
   - Type: `str`
   - Default: `'your-llm-config-group'`
   - Description: The name of the LLM config to use
 
-**ActionSpace Configuration**
+### ActionSpace Configuration
 - `function_calling`
   - Type: `bool`
   - Default: `true`
@@ -373,7 +331,7 @@ The agent configuration options are defined in the `[agent]` and `[agent.<agent_
   - Default: `false`
   - Description: Whether Jupyter is enabled in the action space
 
-**Microagent Usage**
+### Microagent Usage
 - `use_microagents`
   - Type: `bool`
   - Default: `true`
@@ -390,7 +348,7 @@ The sandbox configuration options are defined in the `[sandbox]` section of the
 
 To use these with the docker command, pass in `-e SANDBOX_<option>`. Example: `-e SANDBOX_TIMEOUT`.
 
-**Execution**
+### Execution
 - `timeout`
   - Type: `int`
   - Default: `120`
@@ -401,19 +359,19 @@ To use these with the docker command, pass in `-e SANDBOX_<option>`. Example: `-
   - Default: `1000`
   - Description: Sandbox user ID
 
-**Container Image**
+### Container Image
 - `base_container_image`
   - Type: `str`
   - Default: `"nikolaik/python-nodejs:python3.12-nodejs22"`
   - Description: Container image to use for the sandbox
 
-**Networking**
+### Networking
 - `use_host_network`
   - Type: `bool`
   - Default: `false`
   - Description: Use host network
 
-**Linting and Plugins**
+### Linting and Plugins
 - `enable_auto_lint`
   - Type: `bool`
   - Default: `false`
@@ -424,7 +382,7 @@ To use these with the docker command, pass in `-e SANDBOX_<option>`. Example: `-
   - Default: `true`
   - Description: Whether to initialize plugins
 
-**Dependencies and Environment**
+### Dependencies and Environment
 - `runtime_extra_deps`
   - Type: `str`
   - Default: `""`
@@ -435,7 +393,7 @@ To use these with the docker command, pass in `-e SANDBOX_<option>`. Example: `-
   - Default: `{}`
   - Description: Environment variables to set at the launch of the runtime
 
-**Evaluation**
+### Evaluation
 - `browsergym_eval_env`
   - Type: `str`
   - Default: `""`
@@ -447,13 +405,13 @@ The security configuration options are defined in the `[security]` section of th
 
 To use these with the docker command, pass in `-e SECURITY_<option>`. Example: `-e SECURITY_CONFIRMATION_MODE`.
 
-**Confirmation Mode**
+### Confirmation Mode
 - `confirmation_mode`
   - Type: `bool`
   - Default: `false`
   - Description: Enable confirmation mode
 
-**Security Analyzer**
+### Security Analyzer
 - `security_analyzer`
   - Type: `str`
   - Default: `""`

docs/modules/usage/how-to/cli-mode.md

@@ -58,7 +58,7 @@ Here are some examples of CLI commands and their expected outputs:
 ### Example 1: Simple Task
 
 ```bash
-How can I help? >> Write a Python script that prints "Hello, World!"
+>> Write a Python script that prints "Hello, World!"
 ```
 
 Expected Output:
@@ -72,7 +72,7 @@ Expected Output:
 ### Example 2: Bash Command
 
 ```bash
-How can I help? >> Create a directory named "test_dir"
+>> Create a directory named "test_dir"
 ```
 
 Expected Output:
@@ -86,7 +86,7 @@ Expected Output:
 ### Example 3: Error Handling
 
 ```bash
-How can I help? >> Delete a non-existent file
+>> Delete a non-existent file
 ```
 
 Expected Output:

docs/modules/usage/how-to/gui-mode.md

@@ -76,18 +76,18 @@ When using OpenHands in online mode, the GitHub OAuth flow:
 
 Common issues and solutions:
 
-1. **Token Not Recognized**:
+- **Token Not Recognized**:
    - Ensure the token is properly saved in settings.
    - Check that the token hasn't expired.
    - Verify the token has the required scopes.
    - Try regenerating the token.
 
-2. **Organization Access Denied**:
+- **Organization Access Denied**:
    - Check if SSO is required but not enabled.
    - Verify organization membership.
    - Contact organization admin if token policies are blocking access.
 
-3. **Verifying Token Works**:
+- **Verifying Token Works**:
    - The app will show a green checkmark if the token is valid.
    - Try accessing a repository to confirm permissions.
    - Check the browser console for any error messages.

docs/modules/usage/prompting/microagents-overview.md

@@ -0,0 +1,11 @@
+# Micro-Agents Overview
+
+OpenHands uses specialized micro-agents to handle specific tasks and contexts efficiently. These micro-agents are small,
+focused components that provide specialized behavior and knowledge for particular scenarios.
+
+## Micro-Agent Types
+
+Currently OpenHands supports the following types of Micro-Agents:
+
+* [Public Micro-Agents](./microagents-public): Universal guidelines integrated into OpenHands.
+* [Repository Micro-Agents](./microagents-repo): Repository-specific context and guidelines for OpenHands.

docs/modules/usage/prompting/microagents-public.md

@@ -1,8 +1,5 @@
 # Public Micro-Agents
 
-OpenHands uses specialized micro-agents to handle specific tasks and contexts efficiently. These micro-agents are small,
-focused components that provide specialized behavior and knowledge for particular scenarios.
-
 ## Overview
 
 Public micro-agents are defined in markdown files under the