diff --git a/dev/generate_cli_docs.py b/dev/generate_cli_docs.py
index 4801f55e7..0ab2da138 100644
--- a/dev/generate_cli_docs.py
+++ b/dev/generate_cli_docs.py
@@ -194,6 +194,11 @@ def generate_command_docs(cmd: click.Group) -> str:
 
     markdown_content = []
 
+    # Disable lint warnings for about "first line in file should be a top level heading"
+    # We intentionally start with a level 2 heading below, as this file is imported into another file.
+    markdown_content.append("<!-- markdownlint-disable MD041 -->")
+    markdown_content.append("")
+
     # Add top-level heading to satisfy MD041 linting rule
     markdown_content.append("## Subcommands Reference")
     markdown_content.append("")
diff --git a/docs/docs/core/cli-commands.md b/docs/docs/core/cli-commands.md
index 31e245ac5..96b9dd48f 100644
--- a/docs/docs/core/cli-commands.md
+++ b/docs/docs/core/cli-commands.md
@@ -1,3 +1,5 @@
+<!-- markdownlint-disable MD041 -->
+
 ## Subcommands Reference
 
 ### `drop`
@@ -115,6 +117,7 @@ cocoindex server [OPTIONS] APP_TARGET
 | `-cl, --cors-local INTEGER` | Allow `http://localhost:<port>` to access the server. |
 | `-L, --live-update` | Continuously watch changes from data sources and apply to the target index. |
 | `--setup` | Automatically setup backends for the flow if it's not setup yet. |
+| `--reset` | Drop existing setup before starting server (equivalent to running 'cocoindex drop' first). |
 | `--reexport` | Reexport to targets even if there's no change. |
 | `-f, --force` | Force setup without confirmation prompts. |
 | `-q, --quiet` | Avoid printing anything to the standard output, e.g. statistics. |
@@ -142,6 +145,7 @@ cocoindex setup [OPTIONS] APP_TARGET
 | Option | Description |
 |--------|-------------|
 | `-f, --force` | Force setup without confirmation prompts. |
+| `--reset` | Drop existing setup before running setup (equivalent to running 'cocoindex drop' first). |
 | `--help` | Show this message and exit. |
 
 ---
@@ -203,6 +207,7 @@ cocoindex update [OPTIONS] APP_FLOW_SPECIFIER
 | `-L, --live` | Continuously watch changes from data sources and apply to the target index. |
 | `--reexport` | Reexport to targets even if there's no change. |
 | `--setup` | Automatically setup backends for the flow if it's not setup yet. |
+| `--reset` | Drop existing setup before updating (equivalent to running 'cocoindex drop' first). |
 | `-f, --force` | Force setup without confirmation prompts. |
 | `-q, --quiet` | Avoid printing anything to the standard output, e.g. statistics. |
 | `--help` | Show this message and exit. |