fix: extract additionalArgs as raw CLI arguments instead of --additionalArgs=value

Previously, `additionalArgs` (e.g., `["--sarif-include-query-help=always"]`)
stayed in the options object and was processed by `buildCodeQLArgs` into
`--additionalArgs=--sarif-include-query-help=always`, which is invalid.

Now `additionalArgs` is extracted from options before CLI arg building and
appended as raw arguments after positional args, so args like
`--sarif-include-query-help=always` and `--no-sarif-minify` are passed
through correctly to the `codeql` CLI.

Agent-Logs-Url: https://github.com/advanced-security/codeql-development-mcp-server/sessions/ff382e0c-2894-422a-a9c8-22c431c9a77a

Co-authored-by: data-douser <70299490+data-douser@users.noreply.github.com>

Author: Copilot