docs: fix page links (#2303)

* add agent documentation

* docs changes

* add more docs

* fix typo

* docs cleanups

* blah

Author: chaynabors

docs/native-tools.md

@@ -2,13 +2,13 @@
 
 - [`execute_bash`](#the_execute_bash_tool) — Execute a shell command.
 - [`fs_read`](#the_fs_read_tool) — Read files, directories, and images.
-- [`fs_write`](#the_fs_write_tool) — Create and edit files.
-- [`gh_issue`](#the_gh_issue_tool) — Open a GitHub issue template.
-- [`knowledge`](#the_knowledge_tool) — Store and retrieve information in a knowledge base.
-- [`thinking`](#the_thinking_tool) — Internal reasoning mechanism.
-- [`use_aws`](#the_use_aws_tool) — Make AWS CLI API calls.
+- [`fs_write`](#the-fs-write-tool) — Create and edit files.
+- [`gh_issue`](#the-gh-issue-tool) — Open a GitHub issue template.
+- [`knowledge`](#the-knowledge-tool) — Store and retrieve information in a knowledge base.
+- [`thinking`](#the-thinking-tool) — Internal reasoning mechanism.
+- [`use_aws`](#the-use-aws-tool) — Make AWS CLI API calls.
 
-## The `execute_bash` tool
+### The `execute_bash` tool
 
 Execute the specified bash command.
 
@@ -42,7 +42,7 @@ Execute the specified bash command.
 }
 ```
 
-## The `fs_read` tool
+### The `fs_read` tool
 
 Tool for reading files, directories and images.
 
@@ -71,7 +71,7 @@ Tool for reading files, directories and images.
 }
 ```
 
-## The `fs_write` tool
+### The `fs_write` tool
 
 Tool for creating and editing files.
 
@@ -104,25 +104,25 @@ Tool for creating and editing files.
 }
 ```
 
-## The `gh_issue` tool
+### The `gh_issue` tool
 
 Opens the browser to our GitHub template for reporting issues with `q`.
 
 This tool has no configuration.
 
-## The `knowledge` tool
+### The `knowledge` tool
 
 Store and retrieve information in knowledge base across chat sessions
 
 This tool has no configuration.
 
-## The `thinking` tool
+### The `thinking` tool
 
 Thinking is an internal reasoning mechanism improving the quality of complex tasks by breaking their atomic actions down.
 
 This tool has no configuration.
 
-## The `use_aws` tool
+### The `use_aws` tool
 
 Make an AWS CLI api call with the specified service, operation, and parameters.