diff --git a/Cargo.toml b/Cargo.toml
index c8f806f..c60f097 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -77,3 +77,4 @@ missing_errors_doc = "allow"
 similar_names = "allow"
 missing_panics_doc = "allow"
 module_name_repetitions = "allow"
+struct-excessive-bools = "allow"
diff --git a/src/config.rs b/src/config.rs
index 3d69bd6..c419c2e 100644
--- a/src/config.rs
+++ b/src/config.rs
@@ -28,6 +28,11 @@ pub enum NewConfigError {
     FileDoesNotParseError(#[from] toml::de::Error),
     #[error("ReplacePair compilation error")]
     ReplacePairCompilationError(#[from] ReplacePairCompilationError),
+    #[error("Pages directory missing")]
+    #[help("Please provide a pages directory argument in either your cli or config file")]
+    PagesDirectoryMissing,
+    #[error("Mutually exclusive options: {0} and {1}")]
+    MutuallyExclusiveError(String, String),
     #[error("No files were passed to the config")]
     NoFilesPassedError,
 }
@@ -74,6 +79,9 @@ pub struct Config {
     /// See [`self::cli::Config::allow_dirty`]
     #[builder(default = false)]
     pub allow_dirty: bool,
+    /// See [`self::cli::Config::allow_staged`]
+    #[builder(default = false)]
+    pub allow_staged: bool,
     /// See [`self::file::Config::ignore_word_pairs`]
     #[builder(default = vec![])]
     pub ignore_word_pairs: Vec<(String, String)>,
@@ -101,7 +109,8 @@ pub trait Partial {
         &self,
     ) -> Option<Result<ReplacePair<Alias, FilenameLowercase>, ReplacePairCompilationError>>;
     fn fix(&self) -> Option<bool>;
-    fn allow_dirty(&self) -> Option<bool>;
+    fn allow_dirty(&self) -> Result<Option<bool>, NewConfigError>;
+    fn allow_staged(&self) -> Result<Option<bool>, NewConfigError>;
     fn ignore_word_pairs(&self) -> Option<Vec<(String, String)>>;
     fn ignore_remaining(&self) -> Option<bool>;
 }
@@ -177,7 +186,8 @@ fn combine_partials(
             }
         })
         .maybe_fix(cli_config.fix().or(file_config.fix()))
-        .maybe_allow_dirty(cli_config.allow_dirty().or(file_config.allow_dirty()))
+        .maybe_allow_dirty(cli_config.allow_dirty()?.or(file_config.allow_dirty()?))
+        .maybe_allow_staged(cli_config.allow_staged()?.or(file_config.allow_staged()?))
         .maybe_ignore_word_pairs(
             cli_config
                 .ignore_word_pairs()
diff --git a/src/config/cli.rs b/src/config/cli.rs
index 4c272ee..6c14b32 100644
--- a/src/config/cli.rs
+++ b/src/config/cli.rs
@@ -2,6 +2,7 @@ use clap::Parser;
 use std::path::PathBuf;
 
 use crate::{
+    config::NewConfigError,
     file::{
         content::wikilink::Alias,
         name::{Filename, FilenameLowercase},
@@ -57,10 +58,19 @@ pub struct Config {
     pub fix: bool,
 
     /// Whether or not to allow fixing in a "dirty" git repo, meaning
-    /// the git repo has uncommitted changes
+    /// the git repo has uncommitted changes and those changes will be overwritten by this apps
+    /// changes without user involvement. WARNING: Dangerous
+    /// Mutually exclusive with --allow-staged
     #[clap(long = "allow-dirty")]
     pub allow_dirty: bool,
 
+    /// Whether or not to allow fixing in a "dirty" git repo where everything is "staged", meaning
+    /// the git repo has uncommitted changes, but they still won't be changed by edits unless the
+    /// user stages the changes.
+    /// Mutually exclusive with --allow-dirty
+    #[clap(long = "allow-staged")]
+    pub allow_staged: bool,
+
     /// Ignore remaining errors by adding them to the config
     #[clap(long = "ignore-remaining")]
     pub ignore_remaining: bool,
@@ -110,8 +120,25 @@ impl Partial for Config {
     fn fix(&self) -> Option<bool> {
         Some(self.fix)
     }
-    fn allow_dirty(&self) -> Option<bool> {
-        Some(self.allow_dirty)
+    fn allow_dirty(&self) -> Result<Option<bool>, NewConfigError> {
+        if self.allow_staged && self.allow_dirty {
+            Err(NewConfigError::MutuallyExclusiveError(
+                "allow_staged".to_string(),
+                "allow_dirty".to_string(),
+            ))
+        } else {
+            Ok(Some(self.allow_dirty))
+        }
+    }
+    fn allow_staged(&self) -> Result<Option<bool>, NewConfigError> {
+        if self.allow_staged && self.allow_dirty {
+            Err(NewConfigError::MutuallyExclusiveError(
+                "allow_staged".to_string(),
+                "allow_dirty".to_string(),
+            ))
+        } else {
+            Ok(Some(self.allow_staged))
+        }
     }
     fn ignore_word_pairs(&self) -> Option<Vec<(String, String)>> {
         None
diff --git a/src/config/file.rs b/src/config/file.rs
index 4f57176..bf0c9fb 100644
--- a/src/config/file.rs
+++ b/src/config/file.rs
@@ -199,8 +199,11 @@ impl Partial for Config {
     fn fix(&self) -> Option<bool> {
         None
     }
-    fn allow_dirty(&self) -> Option<bool> {
-        None
+    fn allow_dirty(&self) -> Result<Option<bool>, NewConfigError> {
+        Ok(None)
+    }
+    fn allow_staged(&self) -> Result<Option<bool>, NewConfigError> {
+        Ok(None)
     }
     fn ignore_word_pairs(&self) -> Option<Vec<(String, String)>> {
         if self.ignore_word_pairs.is_empty() {
diff --git a/src/lib.rs b/src/lib.rs
index d0f101d..1504806 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -100,17 +100,40 @@ pub enum OutputErrors {
 
 use git2::{Error, Repository, StatusOptions};
 
-fn is_repo_dirty(repo: &Repository) -> Result<bool, Error> {
-    let mut options = StatusOptions::new();
-    options
-        .include_untracked(true)
-        .recurse_untracked_dirs(true)
-        .exclude_submodules(true)
-        .include_unmodified(false)
-        .include_ignored(false);
+pub enum RepoStatus {
+    Clean,
+    AllStaged,
+    Dirty,
+}
+
+impl RepoStatus {
+    fn get_repo_status(repo: &Repository) -> Result<RepoStatus, Error> {
+        let mut options = StatusOptions::new();
+        options
+            .include_untracked(true)
+            .recurse_untracked_dirs(true)
+            .exclude_submodules(true)
+            .include_unmodified(false)
+            .include_ignored(false);
 
-    let statuses = repo.statuses(Some(&mut options))?;
-    Ok(!statuses.is_empty())
+        let statuses = repo.statuses(Some(&mut options))?;
+        let mut staged = false;
+        let mut dirty = false;
+        for entry in statuses.iter() {
+            let status = entry.status();
+            if status.is_wt_new() || status.is_wt_modified() || status.is_wt_deleted() {
+                dirty = true;
+            }
+            if status.is_index_new() || status.is_index_modified() || status.is_index_deleted() {
+                staged = true;
+            }
+        }
+        match (dirty, staged) {
+            (true, true) => Ok(RepoStatus::AllStaged),
+            (true, false) => Ok(RepoStatus::Dirty),
+            (false, _) => Ok(RepoStatus::Clean),
+        }
+    }
 }
 
 /// Runs [`check`] in a loop until no more fixes can be made
@@ -118,20 +141,28 @@ fn is_repo_dirty(repo: &Repository) -> Result<bool, Error> {
 fn fix(config: &config::Config) -> Result<OutputReport, OutputErrors> {
     // Check if the git repo is dirty
     match git2::Repository::open_from_env() {
-        Ok(git) => match is_repo_dirty(&git) {
-            Ok(is_dirty) => {
-                if !config.allow_dirty && is_dirty {
-                    return Err(OutputErrors::FixError(rules::FixError::DirtyRepo {
-                        backtrace: Backtrace::force_capture(),
-                    }));
-                }
+        Ok(git) => match (
+            RepoStatus::get_repo_status(&git),
+            config.allow_dirty,
+            config.allow_staged,
+        ) {
+            (Ok(RepoStatus::Dirty), false, _) => {
+                return Err(OutputErrors::FixError(rules::FixError::DirtyRepo {
+                    backtrace: Backtrace::force_capture(),
+                }));
+            }
+            (Ok(RepoStatus::AllStaged), _, false) => {
+                return Err(OutputErrors::FixError(rules::FixError::UnstagedChanges {
+                    backtrace: Backtrace::force_capture(),
+                }));
             }
-            Err(e) => {
+            (Err(e), _, _) => {
                 return Err(OutputErrors::FixError(rules::FixError::GitError {
                     source: e,
                     backtrace: Backtrace::force_capture(),
                 }));
             }
+            _ => {}
         },
         Err(e) => {
             return Err(OutputErrors::FixError(rules::FixError::GitError {
diff --git a/src/rules.rs b/src/rules.rs
index 591ced1..1f0f9ad 100644
--- a/src/rules.rs
+++ b/src/rules.rs
@@ -94,6 +94,12 @@ pub enum FixError {
         #[backtrace]
         backtrace: Backtrace,
     },
+    #[error("The git repo has unstaged changes")]
+    #[help("Please stage your changes")]
+    UnstagedChanges {
+        #[backtrace]
+        backtrace: Backtrace,
+    },
     #[error("There was an error checking the git status: {source}")]
     GitError {
         source: git2::Error,