diff --git a/pkgs/by-name/me/mergiraf/Cargo.lock b/pkgs/by-name/me/mergiraf/Cargo.lock
index a7e2ac84ca83..e4bd34d3b5af 100644
--- a/pkgs/by-name/me/mergiraf/Cargo.lock
+++ b/pkgs/by-name/me/mergiraf/Cargo.lock
@@ -1,6 +1,6 @@
 # This file is automatically @generated by Cargo.
 # It is not intended for manual editing.
-version = 3
+version = 4
 
 [[package]]
 name = "adler2"
@@ -108,15 +108,6 @@ version = "2.6.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "b048fb63fd8b5923fc5aa7b340d8e156aec7ec02f0c78fa8a6ddc2613f6f71de"
 
-[[package]]
-name = "block-buffer"
-version = "0.10.4"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "3078c7629b62d3f0439517fa394996acacc5cbc91c5a20d8c658e77abd503a71"
-dependencies = [
- "generic-array",
-]
-
 [[package]]
 name = "bumpalo"
 version = "3.16.0"
@@ -189,7 +180,7 @@ dependencies = [
  "heck",
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn",
 ]
 
 [[package]]
@@ -210,15 +201,6 @@ version = "0.8.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "773648b94d0e5d620f64f280777445740e61fe701025087ec8b57f45c791888b"
 
-[[package]]
-name = "cpufeatures"
-version = "0.2.14"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "608697df725056feaccfa42cffdaeeec3fccc4ffc38358ecd19b243e716a78e0"
-dependencies = [
- "libc",
-]
-
 [[package]]
 name = "crc32fast"
 version = "1.4.2"
@@ -234,16 +216,6 @@ version = "0.8.20"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "22ec99545bb0ed0ea7bb9b8e1e9122ea386ff8a48c0922e43f36d45ab09e0e80"
 
-[[package]]
-name = "crypto-common"
-version = "0.1.6"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "1bfb12502f3fc46cca1bb51ac28df9d618d813cdc3d2f25b9fe775a34af26bb3"
-dependencies = [
- "generic-array",
- "typenum",
-]
-
 [[package]]
 name = "derive_arbitrary"
 version = "1.3.2"
@@ -252,7 +224,7 @@ checksum = "67e77553c4162a157adbf834ebae5b415acbecbeafc7a74b0e886657506a7611"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn",
 ]
 
 [[package]]
@@ -263,7 +235,7 @@ checksum = "5f33878137e4dafd7fa914ad4e259e18a4e8e532b9617a2d0150262bf53abfce"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn",
 ]
 
 [[package]]
@@ -275,16 +247,6 @@ dependencies = [
  "nu-ansi-term",
 ]
 
-[[package]]
-name = "digest"
-version = "0.10.7"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9ed9a281f7bc9b7576e61468ba615a66a5c8cfdff42420a70aa82701a3b1e292"
-dependencies = [
- "block-buffer",
- "crypto-common",
-]
-
 [[package]]
 name = "displaydoc"
 version = "0.2.5"
@@ -293,24 +255,9 @@ checksum = "97369cbbc041bc366949bc74d34658d6cda5621039731c6310521892a3a20ae0"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn",
 ]
 
-[[package]]
-name = "dot-generator"
-version = "0.2.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0aaac7ada45f71873ebce336491d1c1bc4a7c8042c7cea978168ad59e805b871"
-dependencies = [
- "dot-structures",
-]
-
-[[package]]
-name = "dot-structures"
-version = "0.1.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "675e35c02a51bb4d4618cb4885b3839ce6d1787c97b664474d9208d074742e20"
-
 [[package]]
 name = "either"
 version = "1.13.0"
@@ -422,7 +369,7 @@ checksum = "162ee34ebcb7c64a8abebc059ce0fee27c2262618d7b60ed8faf72fef13c3650"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn",
 ]
 
 [[package]]
@@ -461,16 +408,6 @@ dependencies = [
  "slab",
 ]
 
-[[package]]
-name = "generic-array"
-version = "0.14.7"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "85649ca51fd72272d7821adaf274ad91c288277713d9c18820d8499a7ff69e9a"
-dependencies = [
- "typenum",
- "version_check",
-]
-
 [[package]]
 name = "getrandom"
 version = "0.2.15"
@@ -488,22 +425,6 @@ version = "0.3.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "d2fabcfbdc87f4758337ca535fb41a6d701b65693ce38287d856d1674551ec9b"
 
-[[package]]
-name = "graphviz-rust"
-version = "0.9.3"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8f7892a4538fc9aa3658ae6962774428487c16e11663c58c594357975377c901"
-dependencies = [
- "dot-generator",
- "dot-structures",
- "into-attr",
- "into-attr-derive",
- "pest",
- "pest_derive",
- "rand",
- "tempfile",
-]
-
 [[package]]
 name = "hashbrown"
 version = "0.12.3"
@@ -589,28 +510,6 @@ dependencies = [
  "num-traits",
 ]
 
-[[package]]
-name = "into-attr"
-version = "0.1.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "18b48c537e49a709e678caec3753a7dba6854661a1eaa27675024283b3f8b376"
-dependencies = [
- "dot-structures",
-]
-
-[[package]]
-name = "into-attr-derive"
-version = "0.2.1"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ecac7c1ae6cd2c6a3a64d1061a8bdc7f52ff62c26a831a2301e54c1b5d70d5b1"
-dependencies = [
- "dot-generator",
- "dot-structures",
- "into-attr",
- "quote",
- "syn 1.0.109",
-]
-
 [[package]]
 name = "is-terminal"
 version = "0.4.13"
@@ -687,18 +586,19 @@ checksum = "78ca9ab1a0babb1e7d5695e3530886289c18cf2f87ec19a575a0abdce112e3a3"
 
 [[package]]
 name = "mergiraf"
-version = "0.3.0"
+version = "0.4.0"
 dependencies = [
  "cc",
  "clap",
  "diffy",
+ "either",
  "etcetera",
- "graphviz-rust",
  "itertools 0.13.0",
  "log",
  "rand",
  "regex",
  "rstest",
+ "rustc-hash 2.0.0",
  "stderrlog",
  "tempfile",
  "tree-edit-distance",
@@ -711,7 +611,11 @@ dependencies = [
  "tree-sitter-java",
  "tree-sitter-javascript",
  "tree-sitter-json",
+ "tree-sitter-python",
  "tree-sitter-rust",
+ "tree-sitter-scala",
+ "tree-sitter-toml-ng",
+ "tree-sitter-typescript",
  "tree-sitter-xml",
  "tree-sitter-yaml",
  "typed-arena",
@@ -762,55 +666,10 @@ dependencies = [
  "integer-sqrt",
  "itertools 0.10.5",
  "num-traits",
- "rustc-hash",
+ "rustc-hash 1.1.0",
  "thiserror",
 ]
 
-[[package]]
-name = "pest"
-version = "2.7.14"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "879952a81a83930934cbf1786752d6dedc3b1f29e8f8fb2ad1d0a36f377cf442"
-dependencies = [
- "memchr",
- "thiserror",
- "ucd-trie",
-]
-
-[[package]]
-name = "pest_derive"
-version = "2.7.14"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d214365f632b123a47fd913301e14c946c61d1c183ee245fa76eb752e59a02dd"
-dependencies = [
- "pest",
- "pest_generator",
-]
-
-[[package]]
-name = "pest_generator"
-version = "2.7.14"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "eb55586734301717aea2ac313f50b2eb8f60d2fc3dc01d190eefa2e625f60c4e"
-dependencies = [
- "pest",
- "pest_meta",
- "proc-macro2",
- "quote",
- "syn 2.0.85",
-]
-
-[[package]]
-name = "pest_meta"
-version = "2.7.14"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b75da2a70cf4d9cb76833c990ac9cd3923c9a8905a8929789ce347c84564d03d"
-dependencies = [
- "once_cell",
- "pest",
- "sha2",
-]
-
 [[package]]
 name = "pin-project-lite"
 version = "0.2.15"
@@ -926,9 +785,9 @@ checksum = "ba39f3699c378cd8970968dcbff9c43159ea4cfbd88d43c00b22f2ef10a435d2"
 
 [[package]]
 name = "rstest"
-version = "0.21.0"
+version = "0.23.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9afd55a67069d6e434a95161415f5beeada95a01c7b815508a82dcb0e1593682"
+checksum = "0a2c585be59b6b5dd66a9d2084aa1d8bd52fbdb806eafdeffb52791147862035"
 dependencies = [
  "futures",
  "futures-timer",
@@ -938,9 +797,9 @@ dependencies = [
 
 [[package]]
 name = "rstest_macros"
-version = "0.21.0"
+version = "0.23.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "4165dfae59a39dd41d8dec720d3cbfbc71f69744efb480a3920f5d4e0cc6798d"
+checksum = "825ea780781b15345a146be27eaefb05085e337e869bff01b4306a4fd4a9ad5a"
 dependencies = [
  "cfg-if",
  "glob",
@@ -950,7 +809,7 @@ dependencies = [
  "regex",
  "relative-path",
  "rustc_version",
- "syn 2.0.85",
+ "syn",
  "unicode-ident",
 ]
 
@@ -960,6 +819,12 @@ version = "1.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "08d43f7aa6b08d49f382cde6a7982047c3426db949b1424bc4b7ec9ae12c6ce2"
 
+[[package]]
+name = "rustc-hash"
+version = "2.0.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "583034fd73374156e66797ed8e5b0d5690409c9226b22d87cb7f19821c05d152"
+
 [[package]]
 name = "rustc_version"
 version = "0.4.1"
@@ -988,17 +853,6 @@ version = "1.0.23"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "61697e0a1c7e512e84a621326239844a24d8207b4669b41bc18b32ea5cbf988b"
 
-[[package]]
-name = "sha2"
-version = "0.10.8"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "793db75ad2bcafc3ffa7c68b215fee268f537982cd901d132f89c6343f3a3dc8"
-dependencies = [
- "cfg-if",
- "cpufeatures",
- "digest",
-]
-
 [[package]]
 name = "shlex"
 version = "1.3.0"
@@ -1045,17 +899,6 @@ version = "0.11.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "7da8b5736845d9f2fcb837ea5d9e2628564b3b043a70948a3f0b778838c5fb4f"
 
-[[package]]
-name = "syn"
-version = "1.0.109"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237"
-dependencies = [
- "proc-macro2",
- "quote",
- "unicode-ident",
-]
-
 [[package]]
 name = "syn"
 version = "2.0.85"
@@ -1106,7 +949,7 @@ checksum = "ae71770322cbd277e69d762a16c444af02aa0575ac0d174f0b9562d3b37f8602"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn",
 ]
 
 [[package]]
@@ -1247,6 +1090,16 @@ version = "0.1.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e8ddffe35a0e5eeeadf13ff7350af564c6e73993a24db62caee1822b185c2600"
 
+[[package]]
+name = "tree-sitter-python"
+version = "0.23.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2416de7eea3f2e1bd53c250f2d3f3394fc77f78497680f37f4b87918b8d752e3"
+dependencies = [
+ "cc",
+ "tree-sitter-language",
+]
+
 [[package]]
 name = "tree-sitter-rust"
 version = "0.23.0"
@@ -1257,10 +1110,41 @@ dependencies = [
  "tree-sitter-language",
 ]
 
+[[package]]
+name = "tree-sitter-scala"
+version = "0.23.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ab837c0df7ffb6c315fd1cd792164375b3ec0c282ea35f639231f138044f8d0c"
+dependencies = [
+ "cc",
+ "tree-sitter-language",
+]
+
+[[package]]
+name = "tree-sitter-toml-ng"
+version = "0.6.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "695d20cd83acf16c02c773f03e76d7b43b19883d4e2ce3652a8f06b5e0da7455"
+dependencies = [
+ "cc",
+ "tree-sitter",
+]
+
+[[package]]
+name = "tree-sitter-typescript"
+version = "0.23.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6c5f76ed8d947a75cc446d5fccd8b602ebf0cde64ccf2ffa434d873d7a575eff"
+dependencies = [
+ "cc",
+ "tree-sitter-language",
+]
+
 [[package]]
 name = "tree-sitter-xml"
 version = "0.7.0"
-source = "git+https://github.com/tree-sitter-grammars/tree-sitter-xml.git?rev=cd1316e476ec40da6ce1fb5749c9d7e6b4f1090c#cd1316e476ec40da6ce1fb5749c9d7e6b4f1090c"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e670041f591d994f54d597ddcd8f4ebc930e282c4c76a42268743b71f0c8b6b3"
 dependencies = [
  "cc",
  "tree-sitter-language",
@@ -1282,18 +1166,6 @@ version = "2.0.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "6af6ae20167a9ece4bcb41af5b80f8a1f1df981f6391189ce00fd257af04126a"
 
-[[package]]
-name = "typenum"
-version = "1.17.0"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "42ff0bf0c66b8238c6f3b578df37d0b7848e55df8577b3f74f92a69acceeb825"
-
-[[package]]
-name = "ucd-trie"
-version = "0.1.7"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2896d95c02a80c6d6a5d6e953d479f5ddf2dfdb6a244441010e373ac0fb88971"
-
 [[package]]
 name = "unicode-ident"
 version = "1.0.13"
@@ -1306,12 +1178,6 @@ version = "0.2.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "06abde3611657adf66d383f00b093d7faecc7fa57071cce2578660c9f1010821"
 
-[[package]]
-name = "version_check"
-version = "0.9.5"
-source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0b928f33d975fc6ad9f86c8f283853ad26bdd5b10b7f1542aa2fa15e2289105a"
-
 [[package]]
 name = "wasi"
 version = "0.11.0+wasi-snapshot-preview1"
@@ -1340,7 +1206,7 @@ dependencies = [
  "once_cell",
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn",
  "wasm-bindgen-shared",
 ]
 
@@ -1362,7 +1228,7 @@ checksum = "26c6ab57572f7a24a4985830b120de1594465e5d500f24afe89e16b4e833ef68"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn",
  "wasm-bindgen-backend",
  "wasm-bindgen-shared",
 ]
@@ -1566,7 +1432,7 @@ checksum = "fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.85",
+ "syn",
 ]
 
 [[package]]
diff --git a/pkgs/by-name/me/mergiraf/package.nix b/pkgs/by-name/me/mergiraf/package.nix
index 6e888e0bfa21..89c2ccf19aed 100644
--- a/pkgs/by-name/me/mergiraf/package.nix
+++ b/pkgs/by-name/me/mergiraf/package.nix
@@ -11,21 +11,18 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "mergiraf";
-  version = "0.3.0";
+  version = "0.4.0";
 
   src = fetchFromGitea {
     domain = "codeberg.org";
     owner = "mergiraf";
     repo = "mergiraf";
     rev = "refs/tags/v${version}";
-    hash = "sha256-yBLSN5+rPPoxA6Bn1O2NNGNo9cDfowZdaOtVvvUmNAM=";
+    hash = "sha256-ft3lr+k/EOfYO9z8XPgONiUd8YLn6t7D6OsnMxVETrg=";
   };
 
   cargoLock = {
     lockFile = ./Cargo.lock;
-    outputHashes = {
-      "tree-sitter-xml-0.7.0" = "sha256-RTWvOUAs3Uql9DKsP1jf9FZZHaZORE40GXd+6g6RQZw=";
-    };
   };
 
   nativeCheckInputs = [