Update CodeQL CLI manual (#43241)

Co-authored-by: Rachael Sewell <rachmari@github.com>
Co-authored-by: Felicity Chapman <felicitymay@github.com>

content/code-security/codeql-cli/codeql-cli-manual/database-init.md

@@ -41,7 +41,9 @@ language pack and store it in the database metadata, such that it won't
 need to be redone at each extraction command. It is not valid to switch
 extractors in the middle of an extraction operation anyway.)
 
-## Primary options
+## Options
+
+### Primary Options
 
 #### `<database>` <!-- markdownlint-disable-line heading-increment -->
 
@@ -74,7 +76,7 @@ as it may recursively delete the entire database directory.
 \[Advanced] Read a Code Scanning configuration file specifying options
 on how to create the CodeQL databases and what queries to run in later
 steps. For more details on the format of this configuration file, refer
-to [AUTOTITLE](/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning). To run queries from
+to [AUTOTITLE](/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/customizing-code-scanning). To run queries from
 this file in a later step, invoke [codeql database analyze](/code-security/codeql-cli/codeql-cli-manual/database-analyze) without any other queries specified.
 
 #### `--[no-]db-cluster`
@@ -159,7 +161,7 @@ default to <https://github.com/>
 #### `--registries-auth-stdin`
 
 Authenticate to GitHub Enterprise Server Container registries by passing
-a comma-separated list of `<registry_url>=<token>` pairs.
+a comma-separated list of \<registry\_url>=\<token> pairs.
 
 For example, you can pass
 `https://containers.GHEHOSTNAME1/v2/=TOKEN1,https://containers.GHEHOSTNAME2/v2/=TOKEN2`