diff --git a/Cargo.lock b/Cargo.lock
index 8029be1..b07f8af 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -2074,6 +2074,7 @@ dependencies = [
  "reqwest",
  "semver",
  "serde",
+ "serde_json",
  "sha1",
  "sha2",
  "tempfile",
@@ -3194,9 +3195,9 @@ dependencies = [
 
 [[package]]
 name = "serde_json"
-version = "1.0.125"
+version = "1.0.128"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "83c8e735a073ccf5be70aa8066aa984eaf2fa000db6c8d0100ae605b366d31ed"
+checksum = "6ff5456707a1de34e7e37f2a6fd3d3f808c318259cbd01ab6377795054b483d8"
 dependencies = [
  "itoa",
  "memchr",
diff --git a/mcmpmgr/Cargo.toml b/mcmpmgr/Cargo.toml
index 8597e13..0761b3f 100644
--- a/mcmpmgr/Cargo.toml
+++ b/mcmpmgr/Cargo.toml
@@ -13,6 +13,7 @@ pathdiff = "0.2.1"
 reqwest = { version = "0.12.5", features = ["json"] }
 semver = { version = "1.0.23", features = ["serde"] }
 serde = { version = "1.0.207", features = ["derive"] }
+serde_json = "1.0.128"
 sha1 = "0.10.6"
 sha2 = "0.10.8"
 tempfile = "3.12.0"
diff --git a/mcmpmgr/src/file_merge.rs b/mcmpmgr/src/file_merge.rs
new file mode 100644
index 0000000..b462962
--- /dev/null
+++ b/mcmpmgr/src/file_merge.rs
@@ -0,0 +1,150 @@
+use std::{any::Any, default, str::FromStr};
+
+#[derive(Debug, Clone, Copy)]
+pub enum FileType {
+    Json,
+    Yaml,
+    Toml,
+}
+
+impl FromStr for FileType {
+    type Err = anyhow::Error;
+
+    fn from_str(s: &str) -> anyhow::Result<Self> {
+        Ok(if s.contains("json") {
+            FileType::Json
+        } else if s.contains("toml") {
+            FileType::Toml
+        } else if s.contains("yaml") || s.contains("yml") {
+            FileType::Yaml
+        } else {
+            anyhow::bail!("Unmergable file type: {s}")
+        })
+    }
+}
+
+fn merge_json(
+    src: &serde_json::Value,
+    dst: &mut serde_json::Value,
+    overwrite_existing: bool,
+) -> anyhow::Result<()> {
+    if src.is_object() && dst.is_object() {
+        let src = src.as_object().unwrap();
+        let dst = dst.as_object_mut().unwrap();
+
+        for (k, v) in src.iter() {
+            if v.is_object() {
+                let dst_v = dst.entry(k).or_insert(serde_json::json!({}));
+                merge_json(v, dst_v, overwrite_existing)?;
+            } else {
+                if overwrite_existing || !dst.contains_key(k) {
+                    dst.insert(k.to_string(), v.clone());
+                }
+            }
+        }
+    } else {
+        // TODO: Keep track of path for better errors
+        anyhow::bail!("Cannot merge non-objects: {src:#?} and {dst:#?}")
+    }
+    Ok(())
+}
+
+#[test]
+fn test_merge_json() {
+    let src = serde_json::json!({
+        "a": 3,
+        "b": {
+            "x": {
+
+            },
+            "y": {
+                "test": "thing"
+            }
+        },
+        "c": {}
+    });
+    let dst = serde_json::json!({
+        "b": {
+            "y": {
+                "test": "something"
+            }
+        },
+        "c": {
+            "foo": "bar"
+        }
+    });
+
+    let mut merged_overwrite = dst.clone();
+    let mut merged_retained = dst.clone();
+    merge_json(&src, &mut merged_overwrite, true).unwrap();
+    merge_json(&src, &mut merged_retained, false).unwrap();
+
+    assert!(
+        merged_overwrite["b"]["y"]["test"] == "thing",
+        "//b/y/test wasn't overwritten with \"thing\". src={}, dst={}",
+        src,
+        merged_overwrite
+    );
+    assert!(
+        merged_overwrite["a"] == 3,
+        "//a was not set to 3. src={}, dst={}",
+        src,
+        merged_overwrite
+    );
+    assert!(
+        merged_overwrite["b"]["x"].is_object(),
+        "//b/x is not an object. src={}, dst={}",
+        src,
+        merged_overwrite
+    );
+    assert!(
+        merged_overwrite["c"]["foo"] == "bar",
+        "//c/foo != bar. src={}, dst={}",
+        src,
+        merged_overwrite
+    );
+
+    assert!(
+        merged_retained["b"]["y"]["test"] == "something",
+        "//b/y/test was overwritten. src={}, dst={}",
+        src,
+        merged_retained
+    );
+    assert!(
+        merged_retained["a"] == 3,
+        "//a was not set to 3. src={}, dst={}",
+        src,
+        merged_retained
+    );
+    assert!(
+        merged_retained["b"]["x"].is_object(),
+        "//b/x is not an object. src={}, dst={}",
+        src,
+        merged_retained
+    );
+    assert!(
+        merged_retained["c"]["foo"] == "bar",
+        "//c/foo != bar. src={}, dst={}",
+        src,
+        merged_retained
+    );
+}
+
+/// Merge `src` into `dst` if it is a supported file type
+fn merge_files(
+    src: &str,
+    dst: &str,
+    overwrite_existing: bool,
+    file_type: FileType,
+) -> anyhow::Result<String> {
+    Ok(match file_type {
+        FileType::Json => {
+            let src_val = serde_json::from_str(src)?;
+            let mut dst_val = serde_json::from_str(dst)?;
+            merge_json(&src_val, &mut dst_val, overwrite_existing)?;
+            dst_val.to_string()
+        }
+        FileType::Yaml => todo!(),
+        FileType::Toml => todo!(),
+    })
+}
diff --git a/mcmpmgr/src/file_meta.rs b/mcmpmgr/src/file_meta.rs
index 27ac9e4..091d789 100644
--- a/mcmpmgr/src/file_meta.rs
+++ b/mcmpmgr/src/file_meta.rs
@@ -1,6 +1,6 @@
 use crate::providers::DownloadSide;
 use serde::{Deserialize, Serialize};
-use std::{fmt::Display, path::{Path, PathBuf}, str::FromStr};
+use std::{fmt::Display, path::Path, str::FromStr};
 
 #[derive(Debug, Clone, Serialize, Deserialize, Hash)]
 pub struct FileMeta {
@@ -9,7 +9,7 @@ pub struct FileMeta {
     /// Which side the files should be applied on
     pub side: DownloadSide,
     /// When to apply the files to the instance
-    pub apply_policy: FileApplyPolicy
+    pub apply_policy: FileApplyPolicy,
 }
 
 #[derive(Debug, Clone, Serialize, Deserialize, Hash, PartialEq, Eq)]
@@ -17,7 +17,11 @@ pub enum FileApplyPolicy {
     /// Always ensure the file or folder exactly matches that defined in the pack
     Always,
     /// Only apply the file or folder if it doesn't already exist in the pack
-    Once
+    Once,
+    /// Merge into folders and files, retaining existing values in files when a file already exists
+    MergeRetain,
+    /// Merge into folders and files, overwriting existing values in files when a file already exists
+    MergeOverwrite,
 }
 
 impl FromStr for FileApplyPolicy {
@@ -27,6 +31,8 @@ impl FromStr for FileApplyPolicy {
         match s.to_ascii_lowercase().as_str() {
             "always" => Ok(Self::Always),
             "once" => Ok(Self::Once),
+            "mergeretain" => Ok(Self::MergeRetain),
+            "mergeoverwrite" => Ok(Self::MergeOverwrite),
             _ => anyhow::bail!("Invalid apply policy {}. Expected one of: always, once", s),
         }
     }
@@ -37,6 +43,8 @@ impl Display for FileApplyPolicy {
         match self {
             Self::Always => write!(f, "Always"),
             Self::Once => write!(f, "Once"),
+            Self::MergeRetain => write!(f, "MergeRetain"),
+            Self::MergeOverwrite => write!(f, "MergeOverwrite"),
         }
     }
 }
diff --git a/mcmpmgr/src/lib.rs b/mcmpmgr/src/lib.rs
index e364a04..6c734e0 100644
--- a/mcmpmgr/src/lib.rs
+++ b/mcmpmgr/src/lib.rs
@@ -1,5 +1,6 @@
-pub mod mod_meta;
+pub mod file_merge;
 pub mod file_meta;
+pub mod mod_meta;
 pub mod modpack;
 pub mod profiles;
 pub mod providers;
diff --git a/mcmpmgr/src/main.rs b/mcmpmgr/src/main.rs
index df3d02e..b8c409e 100644
--- a/mcmpmgr/src/main.rs
+++ b/mcmpmgr/src/main.rs
@@ -1,3 +1,4 @@
+mod file_merge;
 mod file_meta;
 mod mod_meta;
 mod modpack;