diff --git a/Cargo.lock b/Cargo.lock
index e4f4be36..446a59b8 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -195,6 +195,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "0c2cfd7bf8a6017ddaa4e32ffe7403d547790db06bd171c1c53926faab501623"
 dependencies = [
  "clap_builder",
+ "clap_derive",
 ]
 
 [[package]]
@@ -209,6 +210,18 @@ dependencies = [
  "strsim",
 ]
 
+[[package]]
+name = "clap_derive"
+version = "4.5.49"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2a0b5487afeab2deb2ff4e03a807ad1a03ac532ff5a2cee5d86884440c7f7671"
+dependencies = [
+ "heck",
+ "proc-macro2",
+ "quote",
+ "syn",
+]
+
 [[package]]
 name = "clap_lex"
 version = "0.7.5"
@@ -219,6 +232,7 @@ checksum = "b94f61472cee1439c0b966b47e3aca9ae07e45d070759512cd390ea2bebc6675"
 name = "cli-gen"
 version = "2.0.0-rc12"
 dependencies = [
+ "clap",
  "cpp-linter",
  "pyo3",
 ]
diff --git a/bindings/python/src/lib.rs b/bindings/python/src/lib.rs
index a5eb2763..e51951f7 100644
--- a/bindings/python/src/lib.rs
+++ b/bindings/python/src/lib.rs
@@ -20,7 +20,7 @@ fn main(args: Option<Vec<String>>) -> PyResult<()> {
 
 /// The python binding for the cpp_linter package. It only exposes a ``main()`` function
 /// that is used as the entrypoint script.
-#[pymodule]
+#[pymodule(gil_used = false)]
 fn cpp_linter(m: &Bound<'_, PyModule>) -> PyResult<()> {
     m.add_function(wrap_pyfunction!(main, m)?)?;
     Ok(())
diff --git a/cpp-linter/Cargo.toml b/cpp-linter/Cargo.toml
index fdf931ea..38135966 100644
--- a/cpp-linter/Cargo.toml
+++ b/cpp-linter/Cargo.toml
@@ -16,7 +16,7 @@ license.workspace = true
 [dependencies]
 anyhow = "1.0.100"
 chrono = "0.4.42"
-clap = "4.5.50"
+clap = { version = "4.5.50", features = ["derive"] }
 colored = "3.0.0"
 fast-glob = "1.0.0"
 futures = "0.3.31"
diff --git a/cpp-linter/src/cli/mod.rs b/cpp-linter/src/cli/mod.rs
index 630f62bb..4f2fb951 100644
--- a/cpp-linter/src/cli/mod.rs
+++ b/cpp-linter/src/cli/mod.rs
@@ -1,370 +1,408 @@
 //! This module holds the Command Line Interface design.
-use std::path::PathBuf;
+use std::{path::PathBuf, str::FromStr};
 
 // non-std crates
-use clap::builder::{ArgPredicate, BoolishValueParser, FalseyValueParser};
-use clap::{value_parser, Arg, ArgAction, ArgGroup, ArgMatches, Command};
+use clap::{
+    builder::{
+        ArgPredicate, FalseyValueParser, NonEmptyStringValueParser, PossibleValuesParser,
+        TypedValueParser,
+    },
+    value_parser, ArgAction, Args, Parser, Subcommand, ValueEnum,
+};
 
 mod structs;
-pub use structs::{ClangParams, Cli, FeedbackInput, LinesChangedOnly, ThreadComments};
-
-/// Builds and returns the Command Line Interface's argument parsing object.
-pub fn get_arg_parser() -> Command {
-    Command::new("cpp-linter")
-        .subcommand(
-            Command::new("version")
-                .about("Display the cpp-linter version and exit.")
-        )
-        .arg(
-            Arg::new("verbosity")
-                .long("verbosity")
-                .short('v')
-                .default_value("info")
-                .value_parser(["debug", "info"])
-                .help(
-                    "This controls the action's verbosity in the workflow's logs.
-This option does not affect the verbosity of resulting
-thread comments or file annotations.\n\n",
-            ),
-        )
-        .arg(
-            Arg::new("database")
-                .long("database")
-                .short('p')
-                .value_parser(value_parser!(PathBuf))
-                .help_heading("clang-tidy options")
-                .help(
-                    "The path that is used to read a compile command database.
-For example, it can be a CMake build directory in which a file named
-compile_commands.json exists (set `CMAKE_EXPORT_COMPILE_COMMANDS` to `ON`).
-When no build path is specified, a search for compile_commands.json will be
-attempted through all parent paths of the first input file. See [LLVM docs about
-setup tooling](https://clang.llvm.org/docs/HowToSetupToolingForLLVM.html)
-for an example of setting up Clang Tooling on a source tree.",
-            )
-        )
-        .arg(
-            Arg::new("style")
-                .short('s')
-                .long("style")
-                .default_value("llvm")
-                .help_heading("clang-format options")
-                .help(
-                    "The style rules to use.
-
-- Set this to `file` to have clang-format use the closest relative
-  .clang-format file.
-- Set this to a blank string (`''`) to disable using clang-format
-  entirely.
-
-> [!NOTE]
-> If this is not a blank string, then it is also passed to clang-tidy
-> (if [`--tidy_checks`](#-c-tidy-checks) is not `-*`).
-> This is done to ensure suggestions from both clang-tidy and
-> clang-format are consistent.\n\n",
-            ),
-        )
-        .arg(
-            Arg::new("tidy-checks")
-                .short('c')
-                .long("tidy-checks")
-                .default_value(
-                    "boost-*,bugprone-*,performance-*,readability-*,portability-*,modernize-*,clang-analyzer-*,cppcoreguidelines-*",
-                )
-                .help_heading("clang-tidy options")
-                .help(
-                    "A comma-separated list of globs with optional `-` prefix.
-Globs are processed in order of appearance in the list.
-Globs without `-` prefix add checks with matching names to the set,
-globs with the `-` prefix remove checks with matching names from the set of
-enabled checks. This option's value is appended to the value of the 'Checks'
-option in a .clang-tidy file (if any).
-
-- It is possible to disable clang-tidy entirely by setting this option to
-  `'-*'`.
-- It is also possible to rely solely on a .clang-tidy config file by
-  specifying this option as a blank string (`''`).
-
-See also clang-tidy docs for more info.\n\n",
-            ),
-        )
-        .arg(
-            Arg::new("version")
-                .short('V')
-                .long("version")
-                .default_missing_value("NO-VERSION")
-                .num_args(0..=1)
-                .require_equals(true)
-                .default_value("")
-                .help(
-                    "The desired version of the clang tools to use. Accepted options are
-strings which can be 8, 9, 10, 11, 12, 13, 14, 15, 16, 17.
-
-- Set this option to a blank string (`''`) to use the
-  platform's default installed version.
-- This value can also be a path to where the clang tools are
-  installed (if using a custom install location). All paths specified
-  here are converted to absolute.\n\n",
-            ),
-        )
-        .arg(
-            Arg::new("extensions")
-                .short('e')
-                .long("extensions")
-                .value_delimiter(',')
-                .default_value("c,h,C,H,cpp,hpp,cc,hh,c++,h++,cxx,hxx")
-                .help_heading("Source options")
-                .help("A comma-separated list of file extensions to analyze.\n"),
-        )
-        .arg(
-            Arg::new("repo-root")
-                .short('r')
-                .long("repo-root")
-                .default_value(".")
-                .help_heading("Source options")
-                .help(
-                    "The relative path to the repository root directory. This path is
-relative to the runner's `GITHUB_WORKSPACE` environment variable (or
-the current working directory if not using a CI runner).\n\n",
-            ),
-        )
-        .arg(
-            Arg::new("ignore")
-                .short('i')
-                .long("ignore")
-                .value_delimiter('|')
-                .default_value(".github|target")
-                .help_heading("Source options")
-                .help(
-                    "Set this option with path(s) to ignore (or not ignore).
-
-- In the case of multiple paths, you can use `|` to separate each path.
-- There is no need to use `./` for each entry; a blank string (`''`)
-  represents the repo-root path.
-- This can also have files, but the file's path (relative to
-  the [`--repo-root`](#-r-repo-root)) has to be specified with the filename.
-- Submodules are automatically ignored. Hidden directories (beginning
-  with a `.`) are also ignored automatically.
-- Prefix a path with `!` to explicitly not ignore it. This can be
-  applied to a submodule's path (if desired) but not hidden directories.
-- Glob patterns are supported here. Path separators in glob patterns should
-  use `/` because `\\` represents an escaped literal.\n\n",
-            ),
-        )
-        .arg(
-            Arg::new("ignore-tidy")
-                .short('D')
-                .long("ignore-tidy")
-                .value_delimiter('|')
-                .help_heading("clang-tidy options")
-                .help(
-                    "Similar to [`--ignore`](#-i-ignore) but applied
-exclusively to files analyzed by clang-tidy.\n\n",
-            ),
-        )
-        .arg(
-            Arg::new("ignore-format")
-                .short('M')
-                .long("ignore-format")
-                .value_delimiter('|')
-                .help_heading("clang-format options")
-                .help(
-                    "Similar to [`--ignore`](#-i-ignore) but applied
-exclusively to files analyzed by clang-format.\n\n",
-            ),
-        )
-        .arg(
-            Arg::new("lines-changed-only")
-                .short('l')
-                .long("lines-changed-only")
-                .value_parser(["true", "on", "1", "false", "off", "0", "diff"])
-                .default_value("true")
-                .help_heading("Source options")
-                .help(
-                    "This controls what part of the files are analyzed.
-The following values are accepted:
-
-- `false`: All lines in a file are analyzed.
-- `true`: Only lines in the diff that contain additions are analyzed.
-- `diff`: All lines in the diff are analyzed (including unchanged
-  lines but not subtractions).\n\n",
-            ),
-        )
-        .arg(
-            Arg::new("files-changed-only")
-                .short('f')
-                .long("files-changed-only")
-                .default_value_if("lines-changed-only", ArgPredicate::Equals("true".into()), "true")
-                .default_value("false")
-                .value_parser(FalseyValueParser::new())
-                .help_heading("Source options")
-                .help(
-                    "Set this option to false to analyze any source files in the repo.
-This is automatically enabled if
-[`--lines-changed-only`](#-l-lines-changed-only) is enabled.
-
-> [!NOTE]
-> The `GITHUB_TOKEN` should be supplied when running on a
-> private repository with this option enabled, otherwise the runner
-> does not not have the privilege to list the changed files for an event.
->
-> See [Authenticating with the `GITHUB_TOKEN`](
-> https://docs.github.com/en/actions/reference/authentication-in-a-workflow).\n\n",
-            ),
-        )
-        .arg(
-            Arg::new("extra-arg")
-                .long("extra-arg")
-                .short('x')
-                .action(ArgAction::Append)
-                .help_heading("clang-tidy options")
-                .help(
-                    r#"A string of extra arguments passed to clang-tidy for use as
-compiler arguments. This can be specified more than once for each
-additional argument. Recommend using quotes around the value and
-avoid using spaces between name and value (use `=` instead):
-
-```shell
-cpp-linter --extra-arg="-std=c++17" --extra-arg="-Wall"
-```"#,
-            ),
-        )
-        .arg(
-            Arg::new("thread-comments")
-                .long("thread-comments")
-                .short('g')
-                .value_parser(["true", "on", "1", "false", "off", "0", "update"])
-                .default_value("false")
-                .help_heading("feedback options")
-                .help(
-                    "Set this option to true to enable the use of thread comments as feedback.
-Set this to `update` to update an existing comment if one exists;
-the value 'true' will always delete an old comment and post a new one if necessary.
-
-> [!NOTE]
-> To use thread comments, the `GITHUB_TOKEN` (provided by
-> Github to each repository) must be declared as an environment
-> variable.
->
-> See [Authenticating with the `GITHUB_TOKEN`](
-> https://docs.github.com/en/actions/reference/authentication-in-a-workflow).\n\n",
-            ),
-        )
-        .arg(
-            Arg::new("no-lgtm")
-                .long("no-lgtm")
-                .short('t')
-                .value_parser(FalseyValueParser::new())
-                .default_value("true")
-                .help_heading("feedback options")
-                .help(
-                    "Set this option to true or false to enable or disable the use of a
-thread comment that basically says 'Looks Good To Me' (when all checks pass).
-
-> [!IMPORTANT]
-> The [`--thread-comments`](#-g-thread-comments)
-> option also notes further implications.\n\n",
-            ),
-        )
-        .arg(
-            Arg::new("step-summary")
-                .long("step-summary")
-                .short('w')
-                .value_parser(FalseyValueParser::new())
-                .default_value("false")
-                .help_heading("feedback options")
-                .help(
-                    "Set this option to true or false to enable or disable the use of
-a workflow step summary when the run has concluded.\n\n",
-            ),
-        )
-        .arg(
-            Arg::new("file-annotations")
-                .long("file-annotations")
-                .short('a')
-                .value_parser(FalseyValueParser::new())
-                .default_value("true")
-                .help_heading("feedback options")
-                .help(
-                    "Set this option to false to disable the use of
-file annotations as feedback.\n\n",
-            ),
-        )
-        .arg(
-            Arg::new("tidy-review")
-                .long("tidy-review")
-                .short('d')
-                .value_parser(BoolishValueParser::new())
-                .default_value("false")
-                .help_heading("feedback options")
-                .help(
-                    "Set to `true` to enable Pull Request reviews from clang-tidy.\n\n",
-            ),
-        )
-        .arg(
-            Arg::new("format-review")
-                .long("format-review")
-                .short('m')
-                .value_parser(BoolishValueParser::new())
-                .default_value("false")
-                .help_heading("feedback options")
-                .help(
-                    "Set to `true` to enable Pull Request reviews from clang-format.\n\n",
-            ),
-        )
-        .arg(
-            Arg::new("passive-reviews")
-                .long("passive-reviews")
-                .short('R')
-                .value_parser(BoolishValueParser::new())
-                .default_value("false")
-                .help_heading("feedback options")
-                .help(
-                    "Set to `true` to prevent Pull Request reviews from
-approving or requesting changes.\n\n",
-            ),
-        )
-        .arg(
-            Arg::new("files")
-                .action(ArgAction::Append)
-                .help(
-                    "An explicit path to a file.
-This can be specified zero or more times, resulting in a list of files.
-The list of files is appended to the internal list of 'not ignored' files.
-Further filtering can still be applied (see [Source options](#source-options)).",
-            )
-        )
-        .groups([
-            ArgGroup::new("Clang-tidy options")
-                .args(["tidy-checks", "database", "extra-arg", "ignore-tidy"])
-                .multiple(true)
-                .required(false),
-            ArgGroup::new("Clang-format options")
-                .args(["style", "ignore-format"])
-                .multiple(true)
-                .required(false),
-            ArgGroup::new("General options")
-                .args(["verbosity", "version"])
-                .multiple(true)
-                .required(false),
-            ArgGroup::new("Source options")
-                .args(["extensions", "repo-root", "ignore", "lines-changed-only", "files-changed-only"])
-                .multiple(true)
-                .required(false),
-            ArgGroup::new("Feedback options")
-                .args([
-                    "thread-comments",
-                    "no-lgtm",
-                    "step-summary",
-                    "file-annotations",
-                    "tidy-review",
-                    "format-review",
-                    "passive-reviews",
-                ])
-                .multiple(true)
-                .required(false),
-        ])
-        .next_line_help(true)
+pub use structs::{ClangParams, FeedbackInput, LinesChangedOnly, ThreadComments};
+
+#[derive(Debug, Clone, PartialEq, Eq, ValueEnum)]
+pub enum Verbosity {
+    Info,
+    Debug,
+}
+
+impl Verbosity {
+    pub fn is_debug(&self) -> bool {
+        matches!(self, Verbosity::Debug)
+    }
+}
+
+/// A structure to contain parsed CLI options.
+#[derive(Debug, Clone, Parser)]
+#[command(author, about)]
+pub struct Cli {
+    #[command(flatten)]
+    pub general_options: GeneralOptions,
+
+    #[command(flatten)]
+    pub source_options: SourceOptions,
+
+    #[command(flatten)]
+    pub format_options: FormatOptions,
+
+    #[command(flatten)]
+    pub tidy_options: TidyOptions,
+
+    #[command(flatten)]
+    pub feedback_options: FeedbackOptions,
+
+    /// An explicit path to a file.
+    ///
+    /// This can be specified zero or more times, resulting in a list of files.
+    /// The list of files is appended to the internal list of 'not ignored' files.
+    /// Further filtering can still be applied (see [Source options](#source-options)).
+    #[arg(
+        name = "files",
+        value_name = "FILE",
+        action = ArgAction::Append,
+        verbatim_doc_comment,
+    )]
+    pub not_ignored: Option<Vec<String>>,
+
+    #[command(subcommand)]
+    pub commands: Option<CliCommand>,
+}
+
+#[derive(Debug, Subcommand, Clone)]
+pub enum CliCommand {
+    /// Display the version of cpp-linter and exit.
+    Version,
+}
+
+#[derive(Debug, Clone, Args)]
+#[group(id = "General options", multiple = true, required = false)]
+pub struct GeneralOptions {
+    /// The desired version of the clang tools to use.
+    ///
+    /// Accepted options are:
+    ///
+    /// - A semantic major version number from `10` to `21`.
+    /// - A blank string (`''`) to use the platform's default
+    ///   installed version.
+    /// - A path to where the clang tools are
+    ///   installed (if using a custom install location).
+    ///   All paths specified here are converted to absolute.
+    #[arg(
+        short = 'V',
+        long,
+        default_missing_value = "NO-VERSION",
+        default_value = "",
+        num_args = 0..=1,
+        require_equals = true,
+        help_heading = "General options",
+        verbatim_doc_comment,
+    )]
+    pub version: String,
+
+    /// This controls the action's verbosity in the workflow's logs.
+    ///
+    /// This option does not affect the verbosity of resulting
+    /// thread comments or file annotations.
+    #[arg(
+        short = 'v',
+        long,
+        default_value = "info",
+        help_heading = "General options"
+    )]
+    pub verbosity: Verbosity,
+}
+
+#[derive(Debug, Clone, Args)]
+#[group(id = "Source options", multiple = true, required = false)]
+pub struct SourceOptions {
+    /// A comma-separated list of file extensions to analyze.
+    #[arg(
+        short,
+        long,
+        value_delimiter = ',',
+        default_value = "c,h,C,H,cpp,hpp,cc,hh,c++,h++,cxx,hxx",
+        value_parser = NonEmptyStringValueParser::new(),
+        help_heading = "Source options"
+    )]
+    pub extensions: Vec<String>,
+
+    /// The relative path to the repository root directory.
+    ///
+    /// This path is relative to the runner's `GITHUB_WORKSPACE`
+    /// environment variable (or the current working directory if
+    /// not using a CI runner).
+    #[arg(short, long, default_value = ".", help_heading = "Source options")]
+    pub repo_root: String,
+
+    /// This controls what part of the files are analyzed.
+    ///
+    /// The following values are accepted:
+    ///
+    /// - `false`: All lines in a file are analyzed.
+    /// - `true`: Only lines in the diff that contain additions are analyzed.
+    /// - `diff`: All lines in the diff are analyzed (including unchanged
+    ///   lines but not subtractions).
+    #[arg(
+        short,
+        long,
+        default_value = "true",
+        value_parser = PossibleValuesParser::new(
+            ["true", "on", "1", "false", "off", "0", "diff"],
+        ).map(|s| <LinesChangedOnly as FromStr>::from_str(&s).unwrap()),
+        help_heading = "Source options",
+        verbatim_doc_comment,
+    )]
+    pub lines_changed_only: LinesChangedOnly,
+
+    /// Set this option to false to analyze any source files in the repo.
+    ///
+    /// This is automatically enabled if
+    /// [`--lines-changed-only`](#-l-lines-changed-only) is enabled.
+    ///
+    /// > [!NOTE]
+    /// > The `GITHUB_TOKEN` should be supplied when running on a
+    /// > private repository with this option enabled, otherwise the runner
+    /// > does not not have the privilege to list the changed files for an event.
+    /// >
+    /// > See [Authenticating with the `GITHUB_TOKEN`](
+    /// > https://docs.github.com/en/actions/reference/authentication-in-a-workflow).
+    #[arg(
+        short,
+        long,
+        default_value = "false",
+        default_value_if("lines-changed-only", ArgPredicate::Equals("true".into()), "true"),
+        value_parser = FalseyValueParser::new(),
+        help_heading = "Source options",
+        verbatim_doc_comment,
+    )]
+    pub files_changed_only: bool,
+
+    /// Set this option with path(s) to ignore (or not ignore).
+    ///
+    /// - In the case of multiple paths, you can use `|` to separate each path.
+    /// - There is no need to use `./` for each entry; a blank string (`''`)
+    ///   represents the repo-root path.
+    /// - This can also have files, but the file's path (relative to
+    ///   the [`--repo-root`](#-r-repo-root)) has to be specified with the filename.
+    /// - Submodules are automatically ignored. Hidden directories (beginning
+    ///   with a `.`) are also ignored automatically.
+    /// - Prefix a path with `!` to explicitly not ignore it. This can be
+    ///   applied to a submodule's path (if desired) but not hidden directories.
+    /// - Glob patterns are supported here. Path separators in glob patterns should
+    ///   use `/` because `\` represents an escaped literal.
+    #[arg(
+        short,
+        long,
+        value_delimiter = '|',
+        default_value = ".github|target",
+        help_heading = "Source options",
+        verbatim_doc_comment
+    )]
+    pub ignore: Vec<String>,
+}
+
+#[derive(Debug, Clone, Args)]
+#[group(id = "Clang-format options", multiple = true, required = false)]
+pub struct FormatOptions {
+    /// The style rules to use.
+    ///
+    /// - Set this to `file` to have clang-format use the closest relative
+    ///   .clang-format file.
+    /// - Set this to a blank string (`''`) to disable using clang-format
+    ///   entirely.
+    ///
+    /// > [!NOTE]
+    /// > If this is not a blank string, then it is also passed to clang-tidy
+    /// > (if [`--tidy_checks`](#-c-tidy-checks) is not `-*`).
+    /// > This is done to ensure suggestions from both clang-tidy and
+    /// > clang-format are consistent.
+    #[arg(
+        short,
+        long,
+        default_value = "llvm",
+        help_heading = "Clang-format options",
+        verbatim_doc_comment
+    )]
+    pub style: String,
+
+    /// Similar to [`--ignore`](#-i-ignore) but applied
+    /// exclusively to files analyzed by clang-format.
+    #[arg(
+        short = 'M',
+        long,
+        value_delimiter = '|',
+        help_heading = "Clang-format options"
+    )]
+    pub ignore_format: Option<Vec<String>>,
+}
+
+#[derive(Debug, Clone, Args)]
+#[group(id = "Clang-tidy options", multiple = true, required = false)]
+pub struct TidyOptions {
+    /// Similar to [`--ignore`](#-i-ignore) but applied
+    /// exclusively to files analyzed by clang-tidy.
+    #[arg(
+        short = 'D',
+        long,
+        value_delimiter = '|',
+        help_heading = "Clang-tidy options"
+    )]
+    pub ignore_tidy: Option<Vec<String>>,
+
+    /// A comma-separated list of globs with optional `-` prefix.
+    ///
+    /// Globs are processed in order of appearance in the list.
+    /// Globs without `-` prefix add checks with matching names to the set,
+    /// globs with the `-` prefix remove checks with matching names from the set of
+    /// enabled checks. This option's value is appended to the value of the 'Checks'
+    /// option in a .clang-tidy file (if any).
+    ///
+    /// - It is possible to disable clang-tidy entirely by setting this option to
+    ///   `'-*'`.
+    /// - It is also possible to rely solely on a .clang-tidy config file by
+    ///   specifying this option as a blank string (`''`).
+    ///
+    /// See also clang-tidy docs for more info.
+    #[arg(
+        short = 'c',
+        long,
+        default_value = "boost-*,bugprone-*,performance-*,readability-*,portability-*,modernize-*,clang-analyzer-*,cppcoreguidelines-*",
+        help_heading = "Clang-tidy options",
+        verbatim_doc_comment
+    )]
+    pub tidy_checks: String,
+
+    /// The path that is used to read a compile command database.
+    ///
+    /// For example, it can be a CMake build directory in which a file named
+    /// compile_commands.json exists (set `CMAKE_EXPORT_COMPILE_COMMANDS` to `ON`).
+    /// When no build path is specified, a search for compile_commands.json will be
+    /// attempted through all parent paths of the first input file. See [LLVM docs about
+    /// setup tooling](https://clang.llvm.org/docs/HowToSetupToolingForLLVM.html)
+    /// for an example of setting up Clang Tooling on a source tree.
+    #[arg(
+        short = 'p',
+        long,
+        value_name = "PATH",
+        value_parser = value_parser!(PathBuf),
+        help_heading = "Clang-tidy options",
+    )]
+    pub database: Option<PathBuf>,
+
+    /// A string of extra arguments passed to clang-tidy for use as compiler arguments.
+    ///
+    /// This can be specified more than once for each
+    /// additional argument. Recommend using quotes around the value and
+    /// avoid using spaces between name and value (use `=` instead):
+    ///
+    /// ```shell
+    /// cpp-linter --extra-arg="-std=c++17" --extra-arg="-Wall"
+    /// ```
+    #[arg(
+        short = 'x',
+        long,
+        action = ArgAction::Append,
+        help_heading = "Clang-tidy options",
+        verbatim_doc_comment
+    )]
+    pub extra_arg: Vec<String>,
+}
+
+#[derive(Debug, Clone, Args)]
+#[group(id = "Feedback options", multiple = true, required = false)]
+pub struct FeedbackOptions {
+    /// Set this option to true to enable the use of thread comments as feedback.
+    ///
+    /// Set this to `update` to update an existing comment if one exists;
+    /// the value 'true' will always delete an old comment and post a new one
+    /// if necessary.
+    ///
+    /// > [!NOTE]
+    /// > To use thread comments, the `GITHUB_TOKEN` (provided by
+    /// > Github to each repository) must be declared as an environment
+    /// > variable.
+    /// >
+    /// > See [Authenticating with the `GITHUB_TOKEN`](
+    /// > https://docs.github.com/en/actions/reference/authentication-in-a-workflow).
+    #[arg(
+        short = 'g',
+        long,
+        default_value = "false",
+        value_parser = PossibleValuesParser::new(
+            ["true", "on", "1", "false", "off", "0", "update"],
+        ).map(|s| <ThreadComments as FromStr>::from_str(&s).unwrap()),
+        help_heading = "Feedback options",
+        verbatim_doc_comment,
+    )]
+    pub thread_comments: ThreadComments,
+
+    /// Set this option to true or false to enable or disable the use of a
+    /// thread comment that basically says 'Looks Good To Me' (when all checks pass).
+    ///
+    /// > [!IMPORTANT]
+    /// > The [`--thread-comments`](#-g-thread-comments)
+    /// > option also notes further implications.
+    #[arg(
+        short = 't',
+        long,
+        default_value_t = true,
+        action = ArgAction::Set,
+        value_parser = FalseyValueParser::new(),
+        help_heading = "Feedback options",
+        verbatim_doc_comment,
+    )]
+    pub no_lgtm: bool,
+
+    /// Set this option to true or false to enable or disable the use of
+    /// a workflow step summary when the run has concluded.
+    #[arg(
+        short = 'w',
+        long,
+        default_value_t = false,
+        action = ArgAction::Set,
+        value_parser = FalseyValueParser::new(),
+        help_heading = "Feedback options",
+    )]
+    pub step_summary: bool,
+
+    /// Set this option to false to disable the use of
+    /// file annotations as feedback.
+    #[arg(
+        short = 'a',
+        long,
+        default_value_t = true,
+        action = ArgAction::Set,
+        value_parser = FalseyValueParser::new(),
+        help_heading = "Feedback options",
+    )]
+    pub file_annotations: bool,
+
+    /// Set to `true` to enable Pull Request reviews from clang-tidy.
+    #[arg(
+        short = 'd',
+        long,
+        default_value_t = false,
+        action = ArgAction::Set,
+        value_parser = FalseyValueParser::new(),
+        help_heading = "Feedback options",
+    )]
+    pub tidy_review: bool,
+
+    /// Set to `true` to enable Pull Request reviews from clang-format.
+    #[arg(
+        short = 'm',
+        long,
+        default_value_t = false,
+        action = ArgAction::Set,
+        value_parser = FalseyValueParser::new(),
+        help_heading = "Feedback options",
+    )]
+    pub format_review: bool,
+
+    /// Set to `true` to prevent Pull Request reviews from
+    /// approving or requesting changes.
+    #[arg(
+        short = 'R',
+        long,
+        default_value_t = false,
+        action = ArgAction::Set,
+        value_parser = FalseyValueParser::new(),
+        help_heading = "Feedback options",
+    )]
+    pub passive_reviews: bool,
 }
 
 /// Converts the parsed value of the `--extra-arg` option into an optional vector of strings.
@@ -375,19 +413,21 @@ Further filtering can still be applied (see [Source options](#source-options))."
 ///     - each val is appended to a [`Vec`] (by clap crate)
 /// - specified once with multiple space-separated values
 ///     - resulting [`Vec`] is made from splitting at the spaces between
-/// - not specified at all (returns [`None`])
+/// - not specified at all (returns empty [`Vec`])
 ///
 /// It is preferred that the values specified in either situation do not contain spaces and are
 /// quoted:
+///
 /// ```shell
 /// --extra-arg="-std=c++17" --extra-arg="-Wall"
 /// # or equivalently
 /// --extra-arg="-std=c++17 -Wall"
 /// ```
+///
 /// The cpp-linter-action (for Github CI workflows) can only use 1 `extra-arg` input option, so
 /// the value will be split at spaces.
-pub fn convert_extra_arg_val(args: &ArgMatches) -> Vec<String> {
-    let mut val = args.get_many::<String>("extra-arg").unwrap_or_default();
+pub fn convert_extra_arg_val(args: &[String]) -> Vec<String> {
+    let mut val = args.iter();
     if val.len() == 1 {
         // specified once; split and return result
         val.next()
@@ -405,45 +445,39 @@ pub fn convert_extra_arg_val(args: &ArgMatches) -> Vec<String> {
 
 #[cfg(test)]
 mod test {
-    use clap::ArgMatches;
-
-    use super::{convert_extra_arg_val, get_arg_parser, Cli};
-
-    fn parser_args(input: Vec<&str>) -> ArgMatches {
-        let arg_parser = get_arg_parser();
-        arg_parser.get_matches_from(input)
-    }
+    use super::{convert_extra_arg_val, Cli};
+    use clap::Parser;
 
     #[test]
-    fn ignore_blank_extensions() {
-        let args = parser_args(vec!["cpp-linter", "-e", "c,,h"]);
-        let cli = Cli::from(&args);
-        assert!(!cli.extensions.contains(&"".to_string()));
+    fn error_on_blank_extensions() {
+        let cli = Cli::try_parse_from(vec!["cpp-linter", "-e", "c,,h"]);
+        assert!(cli.is_err());
+        println!("{}", cli.unwrap_err());
     }
 
     #[test]
     fn extra_arg_0() {
-        let args = parser_args(vec!["cpp-linter"]);
-        let extras = convert_extra_arg_val(&args);
+        let args = Cli::parse_from(vec!["cpp-linter"]);
+        let extras = convert_extra_arg_val(&args.tidy_options.extra_arg);
         assert!(extras.is_empty());
     }
 
     #[test]
     fn extra_arg_1() {
-        let args = parser_args(vec!["cpp-linter", "--extra-arg='-std=c++17 -Wall'"]);
-        let extra_args = convert_extra_arg_val(&args);
+        let args = Cli::parse_from(vec!["cpp-linter", "--extra-arg='-std=c++17 -Wall'"]);
+        let extra_args = convert_extra_arg_val(&args.tidy_options.extra_arg);
         assert_eq!(extra_args.len(), 2);
         assert_eq!(extra_args, ["-std=c++17", "-Wall"])
     }
 
     #[test]
     fn extra_arg_2() {
-        let args = parser_args(vec![
+        let args = Cli::parse_from(vec![
             "cpp-linter",
             "--extra-arg=-std=c++17",
             "--extra-arg=-Wall",
         ]);
-        let extra_args = convert_extra_arg_val(&args);
+        let extra_args = convert_extra_arg_val(&args.tidy_options.extra_arg);
         assert_eq!(extra_args.len(), 2);
         assert_eq!(extra_args, ["-std=c++17", "-Wall"])
     }
diff --git a/cpp-linter/src/cli/structs.rs b/cpp-linter/src/cli/structs.rs
index 071ee5c6..318601a5 100644
--- a/cpp-linter/src/cli/structs.rs
+++ b/cpp-linter/src/cli/structs.rs
@@ -1,12 +1,12 @@
-use std::{fmt::Display, path::PathBuf};
+use std::{fmt::Display, path::PathBuf, str::FromStr};
 
-use clap::ArgMatches;
+use clap::ValueEnum;
 
-use super::convert_extra_arg_val;
+use super::Cli;
 use crate::{clang_tools::clang_tidy::CompilationUnit, common_fs::FileFilter};
 
 /// An enum to describe `--lines-changed-only` CLI option's behavior.
-#[derive(PartialEq, Clone, Debug, Default)]
+#[derive(PartialEq, Clone, Debug, Default, ValueEnum)]
 pub enum LinesChangedOnly {
     /// All lines are scanned
     #[default]
@@ -17,15 +17,19 @@ pub enum LinesChangedOnly {
     On,
 }
 
-impl LinesChangedOnly {
-    fn from_string(val: &str) -> LinesChangedOnly {
+impl FromStr for LinesChangedOnly {
+    type Err = ();
+
+    fn from_str(val: &str) -> Result<LinesChangedOnly, Self::Err> {
         match val {
-            "true" | "on" | "1" => LinesChangedOnly::On,
-            "diff" => LinesChangedOnly::Diff,
-            _ => LinesChangedOnly::Off,
+            "true" | "on" | "1" => Ok(LinesChangedOnly::On),
+            "diff" => Ok(LinesChangedOnly::Diff),
+            _ => Ok(LinesChangedOnly::Off),
         }
     }
+}
 
+impl LinesChangedOnly {
     pub fn is_change_valid(&self, added_lines: bool, diff_chunks: bool) -> bool {
         match self {
             LinesChangedOnly::Off => true,
@@ -45,100 +49,8 @@ impl Display for LinesChangedOnly {
     }
 }
 
-/// A structure to contain parsed CLI options.
-pub struct Cli {
-    pub version: String,
-    pub verbosity: bool,
-    pub extensions: Vec<String>,
-    pub repo_root: String,
-    pub lines_changed_only: LinesChangedOnly,
-    pub files_changed_only: bool,
-    pub ignore: Vec<String>,
-    pub style: String,
-    pub ignore_format: Option<Vec<String>>,
-    pub ignore_tidy: Option<Vec<String>>,
-    pub tidy_checks: String,
-    pub database: Option<PathBuf>,
-    pub extra_arg: Vec<String>,
-    pub thread_comments: ThreadComments,
-    pub no_lgtm: bool,
-    pub step_summary: bool,
-    pub file_annotations: bool,
-    pub not_ignored: Option<Vec<String>>,
-    pub tidy_review: bool,
-    pub format_review: bool,
-    pub passive_reviews: bool,
-}
-
-impl From<&ArgMatches> for Cli {
-    /// Construct a [`Cli`] instance from a [`ArgMatches`] instance (after options are parsed from CLI).
-    fn from(args: &ArgMatches) -> Self {
-        let ignore = args
-            .get_many::<String>("ignore")
-            .unwrap()
-            .map(|s| s.to_owned())
-            .collect::<Vec<_>>();
-        let ignore_tidy = args
-            .get_many::<String>("ignore-tidy")
-            .map(|val| val.map(|s| s.to_owned()).collect::<Vec<_>>());
-        let ignore_format = args
-            .get_many::<String>("ignore-format")
-            .map(|val| val.map(|s| s.to_owned()).collect::<Vec<_>>());
-        let extra_arg = convert_extra_arg_val(args);
-
-        let lines_changed_only = LinesChangedOnly::from_string(
-            args.get_one::<String>("lines-changed-only")
-                .unwrap()
-                .as_str(),
-        );
-
-        let thread_comments = ThreadComments::from_string(
-            args.get_one::<String>("thread-comments").unwrap().as_str(),
-        );
-
-        let extensions = args
-            .get_many::<String>("extensions")
-            .unwrap()
-            .filter_map(|s| {
-                if s.is_empty() {
-                    // filter out blank extensions here
-                    None
-                } else {
-                    Some(s.to_string())
-                }
-            })
-            .collect::<Vec<_>>();
-
-        Self {
-            version: args.get_one::<String>("version").unwrap().to_owned(),
-            verbosity: args.get_one::<String>("verbosity").unwrap().as_str() == "debug",
-            extensions,
-            repo_root: args.get_one::<String>("repo-root").unwrap().to_owned(),
-            lines_changed_only,
-            files_changed_only: args.get_flag("files-changed-only"),
-            ignore,
-            style: args.get_one::<String>("style").unwrap().to_owned(),
-            ignore_format,
-            ignore_tidy,
-            tidy_checks: args.get_one::<String>("tidy-checks").unwrap().to_owned(),
-            database: args.get_one::<PathBuf>("database").map(|v| v.to_owned()),
-            extra_arg,
-            no_lgtm: args.get_flag("no-lgtm"),
-            step_summary: args.get_flag("step-summary"),
-            thread_comments,
-            file_annotations: args.get_flag("file-annotations"),
-            not_ignored: args
-                .get_many::<String>("files")
-                .map(|files| Vec::from_iter(files.map(|v| v.to_owned()))),
-            tidy_review: args.get_flag("tidy-review"),
-            format_review: args.get_flag("format-review"),
-            passive_reviews: args.get_flag("passive-reviews"),
-        }
-    }
-}
-
 /// An enum to describe `--thread-comments` CLI option's behavior.
-#[derive(PartialEq, Clone, Debug)]
+#[derive(PartialEq, Clone, Debug, ValueEnum)]
 pub enum ThreadComments {
     /// Always post a new comment and delete any outdated ones.
     On,
@@ -149,12 +61,14 @@ pub enum ThreadComments {
     Update,
 }
 
-impl ThreadComments {
-    fn from_string(val: &str) -> ThreadComments {
+impl FromStr for ThreadComments {
+    type Err = ();
+
+    fn from_str(val: &str) -> Result<ThreadComments, Self::Err> {
         match val {
-            "true" | "on" | "1" => ThreadComments::On,
-            "update" => ThreadComments::Update,
-            _ => ThreadComments::Off,
+            "true" | "on" | "1" => Ok(ThreadComments::On),
+            "update" => Ok(ThreadComments::Update),
+            _ => Ok(ThreadComments::Off),
         }
     }
 }
@@ -191,24 +105,26 @@ impl From<&Cli> for ClangParams {
     /// Construct a [`ClangParams`] instance from a [`Cli`] instance.
     fn from(args: &Cli) -> Self {
         ClangParams {
-            tidy_checks: args.tidy_checks.clone(),
-            lines_changed_only: args.lines_changed_only.clone(),
-            database: args.database.clone(),
-            extra_args: args.extra_arg.clone(),
+            tidy_checks: args.tidy_options.tidy_checks.clone(),
+            lines_changed_only: args.source_options.lines_changed_only.clone(),
+            database: args.tidy_options.database.clone(),
+            extra_args: args.tidy_options.extra_arg.clone(),
             database_json: None,
-            style: args.style.clone(),
+            style: args.format_options.style.clone(),
             clang_tidy_command: None,
             clang_format_command: None,
-            tidy_filter: args
-                .ignore_tidy
-                .as_ref()
-                .map(|ignore_tidy| FileFilter::new(ignore_tidy, args.extensions.clone())),
+            tidy_filter: args.tidy_options.ignore_tidy.as_ref().map(|ignore_tidy| {
+                FileFilter::new(ignore_tidy, args.source_options.extensions.clone())
+            }),
             format_filter: args
+                .format_options
                 .ignore_format
                 .as_ref()
-                .map(|ignore_format| FileFilter::new(ignore_format, args.extensions.clone())),
-            tidy_review: args.tidy_review,
-            format_review: args.format_review,
+                .map(|ignore_format| {
+                    FileFilter::new(ignore_format, args.source_options.extensions.clone())
+                }),
+            tidy_review: args.feedback_options.tidy_review,
+            format_review: args.feedback_options.format_review,
         }
     }
 }
@@ -230,14 +146,14 @@ impl From<&Cli> for FeedbackInput {
     /// Construct a [`FeedbackInput`] instance from a [`Cli`] instance.
     fn from(args: &Cli) -> Self {
         FeedbackInput {
-            style: args.style.clone(),
-            no_lgtm: args.no_lgtm,
-            step_summary: args.step_summary,
-            thread_comments: args.thread_comments.clone(),
-            file_annotations: args.file_annotations,
-            tidy_review: args.tidy_review,
-            format_review: args.format_review,
-            passive_reviews: args.passive_reviews,
+            style: args.format_options.style.clone(),
+            no_lgtm: args.feedback_options.no_lgtm,
+            step_summary: args.feedback_options.step_summary,
+            thread_comments: args.feedback_options.thread_comments.clone(),
+            file_annotations: args.feedback_options.file_annotations,
+            tidy_review: args.feedback_options.tidy_review,
+            format_review: args.feedback_options.format_review,
+            passive_reviews: args.feedback_options.passive_reviews,
         }
     }
 }
@@ -260,15 +176,15 @@ impl Default for FeedbackInput {
 
 #[cfg(test)]
 mod test {
-    use crate::cli::get_arg_parser;
+    // use crate::cli::get_arg_parser;
 
     use super::{Cli, LinesChangedOnly, ThreadComments};
+    use clap::Parser;
+    use std::str::FromStr;
 
     #[test]
     fn parse_positional() {
-        let parser = get_arg_parser();
-        let args = parser.get_matches_from(["cpp-linter", "file1.c", "file2.h"]);
-        let cli = Cli::from(&args);
+        let cli = Cli::parse_from(["cpp-linter", "file1.c", "file2.h"]);
         let not_ignored = cli.not_ignored.expect("failed to parse positional args");
         assert!(!not_ignored.is_empty());
         assert!(not_ignored.contains(&String::from("file1.c")));
@@ -279,7 +195,7 @@ mod test {
     fn display_lines_changed_only_enum() {
         let input = "diff".to_string();
         assert_eq!(
-            LinesChangedOnly::from_string(&input),
+            LinesChangedOnly::from_str(&input).unwrap(),
             LinesChangedOnly::Diff
         );
         assert_eq!(format!("{}", LinesChangedOnly::Diff), input);
@@ -288,7 +204,10 @@ mod test {
     #[test]
     fn display_thread_comments_enum() {
         let input = "false".to_string();
-        assert_eq!(ThreadComments::from_string(&input), ThreadComments::Off);
+        assert_eq!(
+            ThreadComments::from_str(&input).unwrap(),
+            ThreadComments::Off
+        );
         assert_eq!(format!("{}", ThreadComments::Off), input);
     }
 }
diff --git a/cpp-linter/src/common_fs/file_filter.rs b/cpp-linter/src/common_fs/file_filter.rs
index fc848cd6..3760013b 100644
--- a/cpp-linter/src/common_fs/file_filter.rs
+++ b/cpp-linter/src/common_fs/file_filter.rs
@@ -183,20 +183,17 @@ impl FileFilter {
 
 #[cfg(test)]
 mod tests {
+    use clap::Parser;
+
     use super::FileFilter;
-    use crate::cli::get_arg_parser;
+    use crate::cli::Cli;
     use std::{env::set_current_dir, path::PathBuf};
 
     // ************* tests for ignored paths
 
     fn setup_ignore(input: &str, extension: Vec<String>) -> FileFilter {
-        let arg_parser = get_arg_parser();
-        let args = arg_parser.get_matches_from(vec!["cpp-linter", "-i", input]);
-        let ignore_arg = args
-            .get_many::<String>("ignore")
-            .unwrap()
-            .map(|s| s.to_owned())
-            .collect::<Vec<_>>();
+        let args = Cli::parse_from(["cpp-linter", "-i", input]);
+        let ignore_arg = args.source_options.ignore;
         let file_filter = FileFilter::new(&ignore_arg, extension);
         println!("ignored = {:?}", file_filter.ignored);
         println!("not ignored = {:?}", file_filter.not_ignored);
diff --git a/cpp-linter/src/run.rs b/cpp-linter/src/run.rs
index e3bf6898..e20bdb3b 100644
--- a/cpp-linter/src/run.rs
+++ b/cpp-linter/src/run.rs
@@ -9,11 +9,12 @@ use std::sync::{Arc, Mutex};
 
 // non-std crates
 use anyhow::{anyhow, Result};
+use clap::Parser;
 use log::{set_max_level, LevelFilter};
 
 // project specific modules/crates
 use crate::clang_tools::capture_clang_tools_output;
-use crate::cli::{get_arg_parser, ClangParams, Cli, FeedbackInput, LinesChangedOnly};
+use crate::cli::{ClangParams, Cli, CliCommand, FeedbackInput, LinesChangedOnly};
 use crate::common_fs::FileFilter;
 use crate::logger;
 use crate::rest_api::{github::GithubApiClient, RestApiClient};
@@ -40,38 +41,45 @@ const VERSION: &str = env!("CARGO_PKG_VERSION");
 /// alias ("path/to/cpp-linter.exe"). Thus, the parser in [`crate::cli`] will halt on an error
 /// because it is not configured to handle positional arguments.
 pub async fn run_main(args: Vec<String>) -> Result<()> {
-    let arg_parser = get_arg_parser();
-    let args = arg_parser.get_matches_from(args);
-    let cli = Cli::from(&args);
+    let cli = Cli::parse_from(args);
 
-    if args.subcommand_matches("version").is_some() {
+    if matches!(cli.commands, Some(CliCommand::Version)) {
         println!("cpp-linter v{}", VERSION);
         return Ok(());
     }
 
     logger::try_init();
 
-    if cli.version == "NO-VERSION" {
+    if cli.general_options.version == "NO-VERSION" {
         log::error!("The `--version` arg is used to specify which version of clang to use.");
         log::error!("To get the cpp-linter version, use `cpp-linter version` sub-command.");
         return Err(anyhow!("Clang version not specified."));
     }
 
-    if cli.repo_root != "." {
-        env::set_current_dir(Path::new(&cli.repo_root))
-            .unwrap_or_else(|_| panic!("'{}' is inaccessible or does not exist", cli.repo_root));
+    if cli.source_options.repo_root != "." {
+        env::set_current_dir(Path::new(&cli.source_options.repo_root)).map_err(|e| {
+            anyhow!(
+                "'{}' is inaccessible or does not exist: {e:?}",
+                cli.source_options.repo_root
+            )
+        })?;
     }
 
     let rest_api_client = GithubApiClient::new()?;
-    set_max_level(if cli.verbosity || rest_api_client.debug_enabled {
-        LevelFilter::Debug
-    } else {
-        LevelFilter::Info
-    });
+    set_max_level(
+        if cli.general_options.verbosity.is_debug() || rest_api_client.debug_enabled {
+            LevelFilter::Debug
+        } else {
+            LevelFilter::Info
+        },
+    );
     log::info!("Processing event {}", rest_api_client.event_name);
     let is_pr = rest_api_client.event_name == "pull_request";
 
-    let mut file_filter = FileFilter::new(&cli.ignore, cli.extensions.clone());
+    let mut file_filter = FileFilter::new(
+        &cli.source_options.ignore,
+        cli.source_options.extensions.clone(),
+    );
     file_filter.parse_submodules();
     if let Some(files) = &cli.not_ignored {
         file_filter.not_ignored.extend(files.clone());
@@ -91,31 +99,32 @@ pub async fn run_main(args: Vec<String>) -> Result<()> {
     }
 
     rest_api_client.start_log_group(String::from("Get list of specified source files"));
-    let files =
-        if !matches!(cli.lines_changed_only, LinesChangedOnly::Off) || cli.files_changed_only {
-            // parse_diff(github_rest_api_payload)
-            rest_api_client
-                .get_list_of_changed_files(&file_filter, &cli.lines_changed_only)
-                .await?
-        } else {
-            // walk the folder and look for files with specified extensions according to ignore values.
-            let mut all_files = file_filter.list_source_files(".")?;
-            if is_pr && (cli.tidy_review || cli.format_review) {
-                let changed_files = rest_api_client
-                    .get_list_of_changed_files(&file_filter, &LinesChangedOnly::Off)
-                    .await?;
-                for changed_file in changed_files {
-                    for file in &mut all_files {
-                        if changed_file.name == file.name {
-                            file.diff_chunks = changed_file.diff_chunks.clone();
-                            file.added_lines = changed_file.added_lines.clone();
-                            file.added_ranges = changed_file.added_ranges.clone();
-                        }
+    let files = if !matches!(cli.source_options.lines_changed_only, LinesChangedOnly::Off)
+        || cli.source_options.files_changed_only
+    {
+        // parse_diff(github_rest_api_payload)
+        rest_api_client
+            .get_list_of_changed_files(&file_filter, &cli.source_options.lines_changed_only)
+            .await?
+    } else {
+        // walk the folder and look for files with specified extensions according to ignore values.
+        let mut all_files = file_filter.list_source_files(".")?;
+        if is_pr && (cli.feedback_options.tidy_review || cli.feedback_options.format_review) {
+            let changed_files = rest_api_client
+                .get_list_of_changed_files(&file_filter, &LinesChangedOnly::Off)
+                .await?;
+            for changed_file in changed_files {
+                for file in &mut all_files {
+                    if changed_file.name == file.name {
+                        file.diff_chunks = changed_file.diff_chunks.clone();
+                        file.added_lines = changed_file.added_lines.clone();
+                        file.added_ranges = changed_file.added_ranges.clone();
                     }
                 }
             }
-            all_files
-        };
+        }
+        all_files
+    };
     let mut arc_files = vec![];
     log::info!("Giving attention to the following files:");
     for file in files {
@@ -130,7 +139,7 @@ pub async fn run_main(args: Vec<String>) -> Result<()> {
     let user_inputs = FeedbackInput::from(&cli);
     let clang_versions = capture_clang_tools_output(
         &mut arc_files,
-        cli.version.as_str(),
+        cli.general_options.version.as_str(),
         &mut clang_params,
         &rest_api_client,
     )
@@ -231,4 +240,16 @@ mod test {
         .await;
         assert!(result.is_ok());
     }
+
+    #[tokio::test]
+    async fn bad_repo_root() {
+        env::remove_var("GITHUB_OUTPUT"); // avoid writing to GH_OUT in parallel-running tests
+        let result = run_main(vec![
+            "cpp-linter".to_string(),
+            "-r".to_string(),
+            "some-non-existent-dir".to_string(),
+        ])
+        .await;
+        assert!(result.is_err());
+    }
 }
diff --git a/docs/Cargo.toml b/docs/Cargo.toml
index 550ec127..57df50d2 100644
--- a/docs/Cargo.toml
+++ b/docs/Cargo.toml
@@ -10,7 +10,8 @@ license.workspace = true
 
 [dependencies]
 cpp-linter = { path = "../cpp-linter" }
-pyo3 = "0.27.1"
+pyo3 = {version = "0.27.1", features = ["extension-module"] }
+clap = { version = "4.5.50", features = ["derive"] }
 
 [lib]
 name = "cli_gen"
diff --git a/docs/pyproject.toml b/docs/pyproject.toml
index 9587a2c7..158fec84 100644
--- a/docs/pyproject.toml
+++ b/docs/pyproject.toml
@@ -6,31 +6,28 @@ build-backend = "maturin"
 name = "cli-gen"
 description = "Generate cpp-linter CLI doc from rust src."
 readme = "README.md"
-license = {text = "MIT License"}
-requires-python = ">=3.7"
+license = "MIT"
+requires-python = ">=3.9"
 authors = [
     { name = "Brendan Doherty", email = "2bndy5@gmail.com" },
 ]
 classifiers = ["Private :: Do Not Upload"]
 dynamic = ["version"]
 
-[tool.maturin]
-features = ["pyo3/extension-module"]
-
 [dependency-groups]
 dev = [
     "maturin==1.9.1",
     "mypy==1.17.0",
     "patchelf==0.17.2.2 ; sys_platform == 'linux'",
-    "ruff==0.12.4",
+    "ruff==0.14.3",
 ]
 docs = [
     "markdown-gfm-admonition==0.1.1",
     "mkdocs==1.6.1",
     "mkdocs-gen-files==0.5.0",
-    "mkdocs-include-markdown-plugin==7.1.6",
-    "mkdocs-material==9.6.15",
-    "pyyaml==6.0.2",
+    "mkdocs-include-markdown-plugin==7.2.0",
+    "mkdocs-material==9.6.22",
+    "pyyaml==6.0.3",
 ]
 
 [tool.uv]
diff --git a/docs/src/lib.rs b/docs/src/lib.rs
index 20e0cce4..109f74ca 100644
--- a/docs/src/lib.rs
+++ b/docs/src/lib.rs
@@ -2,7 +2,8 @@
 //! For actual library/binary source code look in cpp-linter folder.
 use std::collections::HashMap;
 
-use cpp_linter::cli;
+use clap::CommandFactory;
+use cpp_linter::cli::Cli;
 use pyo3::{exceptions::PyValueError, prelude::*};
 
 const GROUPS_ORDER: [&str; 5] = [
@@ -16,7 +17,7 @@ const GROUPS_ORDER: [&str; 5] = [
 #[pyfunction]
 fn generate_cli_doc(metadata: HashMap<String, HashMap<String, Py<PyAny>>>) -> PyResult<String> {
     let mut out = String::new();
-    let mut command = cli::get_arg_parser();
+    let mut command = Cli::command();
     out.push_str(
         format!(
             "```text title=\"Usage\"\n{}\n```\n",
@@ -49,7 +50,8 @@ fn generate_cli_doc(metadata: HashMap<String, HashMap<String, Py<PyAny>>>) -> Py
     out.push_str("## Arguments\n");
     for arg in command.get_positionals() {
         out.push_str(format!("\n### `{}`\n\n", arg.get_id().as_str()).as_str());
-        if let Some(help) = arg.get_help() {
+        let short_help = &arg.get_help();
+        if let Some(help) = arg.get_long_help().or(*short_help) {
             out.push_str(format!("{}\n", help.to_string().trim()).as_str());
         }
     }
@@ -110,7 +112,8 @@ fn generate_cli_doc(metadata: HashMap<String, HashMap<String, Py<PyAny>>>) -> Py
             } else {
                 out.push('\n');
             }
-            if let Some(help) = &arg.get_help() {
+            let short_help = arg.get_help();
+            if let Some(help) = &arg.get_long_help().or(short_help) {
                 out.push_str(format!("{}\n", help.to_string().trim()).as_str());
             }
         }
@@ -118,7 +121,7 @@ fn generate_cli_doc(metadata: HashMap<String, HashMap<String, Py<PyAny>>>) -> Py
     Ok(out)
 }
 
-#[pymodule]
+#[pymodule(gil_used = false)]
 pub fn cli_gen(m: &Bound<'_, PyModule>) -> PyResult<()> {
     m.add_function(wrap_pyfunction!(generate_cli_doc, m)?)?;
     Ok(())
diff --git a/pyproject.toml b/pyproject.toml
index f3a8678d..d0227ca2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,7 +7,7 @@ name = "cpp-linter"
 description = "Run clang-format and clang-tidy on a batch of files."
 readme = "bindings/python/README.md"
 keywords = ["clang", "clang-tools", "linter", "clang-tidy", "clang-format"]
-license = {text = "MIT License"}
+license = "MIT"
 requires-python = ">=3.9"
 authors = [
     { name = "Brendan Doherty", email = "2bndy5@gmail.com" },
@@ -16,7 +16,6 @@ authors = [
 classifiers = [
     # https://pypi.org/pypi?%3Aaction=list_classifiers
     "Development Status :: 5 - Production/Stable",
-    "License :: OSI Approved :: MIT License",
     "Intended Audience :: Developers",
     "Intended Audience :: System Administrators",
     "Intended Audience :: Information Technology",
@@ -57,7 +56,7 @@ dev = [
     "mypy==1.17.0",
     "patchelf==0.17.2.2 ; sys_platform == 'linux'",
     "pre-commit>=4.2.0",
-    "ruff==0.12.4",
+    "ruff==0.14.3",
 ]
 test = [
     "meson==1.8.2",
diff --git a/uv.lock b/uv.lock
index 30f33481..1e540337 100644
--- a/uv.lock
+++ b/uv.lock
@@ -64,77 +64,107 @@ wheels = [
 
 [[package]]
 name = "charset-normalizer"
-version = "3.4.3"
-source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/83/2d/5fd176ceb9b2fc619e63405525573493ca23441330fcdaee6bef9460e924/charset_normalizer-3.4.3.tar.gz", hash = "sha256:6fce4b8500244f6fcb71465d4a4930d132ba9ab8e71a7859e6a5d59851068d14", size = 122371, upload-time = "2025-08-09T07:57:28.46Z" }
-wheels = [
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