diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 3bfd1dfb..dc9a3b41 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -280,7 +280,7 @@ jobs:
 
       - name: Generate DEPENDENCIES.json
         if: github.event_name != 'push'
-        run: npm ls --json --all --omit=dev > DEPENDENCIES.json 2>/dev/null || true
+        run: mkdir -p generated && npm ls --json --all --omit=dev > generated/DEPENDENCIES.json 2>/dev/null || true
 
       - name: Push version bump via PR
         if: github.event_name != 'push'
@@ -292,10 +292,10 @@ jobs:
           BRANCH="release/v${VERSION}"
 
           # Check if there are version bump changes to push
-          if git diff --quiet HEAD -- package.json package-lock.json CHANGELOG.md DEPENDENCIES.json; then
+          if git diff --quiet HEAD -- package.json package-lock.json CHANGELOG.md generated/DEPENDENCIES.json; then
             echo "No version bump commit to push — skipping PR"
           else
-            git add package.json package-lock.json CHANGELOG.md DEPENDENCIES.json
+            git add package.json package-lock.json CHANGELOG.md generated/DEPENDENCIES.json
             git commit -m "chore: release v${VERSION}"
             git push origin "HEAD:refs/heads/${BRANCH}"
             gh pr create \
diff --git a/.gitignore b/.gitignore
index 75b56832..d8bd5118 100644
--- a/.gitignore
+++ b/.gitignore
@@ -8,4 +8,5 @@ grammars/*.wasm
 .claude/codegraph-checked.log
 artifacts/
 pkg/
-DEPENDENCIES.md
+generated/DEPENDENCIES.md
+generated/DEPENDENCIES.json
diff --git a/DEPENDENCIES.json b/DEPENDENCIES.json
deleted file mode 100644
index ce27f43a..00000000
--- a/DEPENDENCIES.json
+++ /dev/null
@@ -1,1379 +0,0 @@
-{
-  "version": "2.2.1",
-  "name": "@optave/codegraph",
-  "problems": [
-    "invalid: @optave/codegraph-linux-x64-gnu@2.1.0 /home/runner/work/codegraph/codegraph/node_modules/@optave/codegraph-linux-x64-gnu"
-  ],
-  "dependencies": {
-    "@huggingface/transformers": {
-      "version": "3.8.1",
-      "resolved": "https://registry.npmjs.org/@huggingface/transformers/-/transformers-3.8.1.tgz",
-      "overridden": false,
-      "dependencies": {
-        "@huggingface/jinja": {
-          "version": "0.5.5",
-          "resolved": "https://registry.npmjs.org/@huggingface/jinja/-/jinja-0.5.5.tgz",
-          "overridden": false
-        },
-        "onnxruntime-node": {
-          "version": "1.21.0",
-          "resolved": "https://registry.npmjs.org/onnxruntime-node/-/onnxruntime-node-1.21.0.tgz",
-          "overridden": false,
-          "dependencies": {
-            "global-agent": {
-              "version": "3.0.0",
-              "resolved": "https://registry.npmjs.org/global-agent/-/global-agent-3.0.0.tgz",
-              "overridden": false,
-              "dependencies": {
-                "boolean": {
-                  "version": "3.2.0",
-                  "resolved": "https://registry.npmjs.org/boolean/-/boolean-3.2.0.tgz",
-                  "overridden": false
-                },
-                "es6-error": {
-                  "version": "4.1.1",
-                  "resolved": "https://registry.npmjs.org/es6-error/-/es6-error-4.1.1.tgz",
-                  "overridden": false
-                },
-                "matcher": {
-                  "version": "3.0.0",
-                  "resolved": "https://registry.npmjs.org/matcher/-/matcher-3.0.0.tgz",
-                  "overridden": false,
-                  "dependencies": {
-                    "escape-string-regexp": {
-                      "version": "4.0.0",
-                      "resolved": "https://registry.npmjs.org/escape-string-regexp/-/escape-string-regexp-4.0.0.tgz",
-                      "overridden": false
-                    }
-                  }
-                },
-                "roarr": {
-                  "version": "2.15.4",
-                  "resolved": "https://registry.npmjs.org/roarr/-/roarr-2.15.4.tgz",
-                  "overridden": false,
-                  "dependencies": {
-                    "boolean": {
-                      "version": "3.2.0"
-                    },
-                    "detect-node": {
-                      "version": "2.1.0",
-                      "resolved": "https://registry.npmjs.org/detect-node/-/detect-node-2.1.0.tgz",
-                      "overridden": false
-                    },
-                    "globalthis": {
-                      "version": "1.0.4",
-                      "resolved": "https://registry.npmjs.org/globalthis/-/globalthis-1.0.4.tgz",
-                      "overridden": false,
-                      "dependencies": {
-                        "define-properties": {
-                          "version": "1.2.1",
-                          "resolved": "https://registry.npmjs.org/define-properties/-/define-properties-1.2.1.tgz",
-                          "overridden": false,
-                          "dependencies": {
-                            "define-data-property": {
-                              "version": "1.1.4",
-                              "resolved": "https://registry.npmjs.org/define-data-property/-/define-data-property-1.1.4.tgz",
-                              "overridden": false,
-                              "dependencies": {
-                                "es-define-property": {
-                                  "version": "1.0.1"
-                                },
-                                "es-errors": {
-                                  "version": "1.3.0"
-                                },
-                                "gopd": {
-                                  "version": "1.2.0"
-                                }
-                              }
-                            },
-                            "has-property-descriptors": {
-                              "version": "1.0.2",
-                              "resolved": "https://registry.npmjs.org/has-property-descriptors/-/has-property-descriptors-1.0.2.tgz",
-                              "overridden": false,
-                              "dependencies": {
-                                "es-define-property": {
-                                  "version": "1.0.1"
-                                }
-                              }
-                            },
-                            "object-keys": {
-                              "version": "1.1.1",
-                              "resolved": "https://registry.npmjs.org/object-keys/-/object-keys-1.1.1.tgz",
-                              "overridden": false
-                            }
-                          }
-                        },
-                        "gopd": {
-                          "version": "1.2.0",
-                          "resolved": "https://registry.npmjs.org/gopd/-/gopd-1.2.0.tgz",
-                          "overridden": false
-                        }
-                      }
-                    },
-                    "json-stringify-safe": {
-                      "version": "5.0.1",
-                      "resolved": "https://registry.npmjs.org/json-stringify-safe/-/json-stringify-safe-5.0.1.tgz",
-                      "overridden": false
-                    },
-                    "semver-compare": {
-                      "version": "1.0.0",
-                      "resolved": "https://registry.npmjs.org/semver-compare/-/semver-compare-1.0.0.tgz",
-                      "overridden": false
-                    },
-                    "sprintf-js": {
-                      "version": "1.1.3",
-                      "resolved": "https://registry.npmjs.org/sprintf-js/-/sprintf-js-1.1.3.tgz",
-                      "overridden": false
-                    }
-                  }
-                },
-                "semver": {
-                  "version": "7.7.4"
-                },
-                "serialize-error": {
-                  "version": "7.0.1",
-                  "resolved": "https://registry.npmjs.org/serialize-error/-/serialize-error-7.0.1.tgz",
-                  "overridden": false,
-                  "dependencies": {
-                    "type-fest": {
-                      "version": "0.13.1",
-                      "resolved": "https://registry.npmjs.org/type-fest/-/type-fest-0.13.1.tgz",
-                      "overridden": false
-                    }
-                  }
-                }
-              }
-            },
-            "onnxruntime-common": {
-              "version": "1.21.0",
-              "resolved": "https://registry.npmjs.org/onnxruntime-common/-/onnxruntime-common-1.21.0.tgz",
-              "overridden": false
-            },
-            "tar": {
-              "version": "7.5.9",
-              "resolved": "https://registry.npmjs.org/tar/-/tar-7.5.9.tgz",
-              "overridden": false,
-              "dependencies": {
-                "@isaacs/fs-minipass": {
-                  "version": "4.0.1",
-                  "resolved": "https://registry.npmjs.org/@isaacs/fs-minipass/-/fs-minipass-4.0.1.tgz",
-                  "overridden": false,
-                  "dependencies": {
-                    "minipass": {
-                      "version": "7.1.3"
-                    }
-                  }
-                },
-                "chownr": {
-                  "version": "3.0.0",
-                  "resolved": "https://registry.npmjs.org/chownr/-/chownr-3.0.0.tgz",
-                  "overridden": false
-                },
-                "minipass": {
-                  "version": "7.1.3",
-                  "resolved": "https://registry.npmjs.org/minipass/-/minipass-7.1.3.tgz",
-                  "overridden": false
-                },
-                "minizlib": {
-                  "version": "3.1.0",
-                  "resolved": "https://registry.npmjs.org/minizlib/-/minizlib-3.1.0.tgz",
-                  "overridden": false,
-                  "dependencies": {
-                    "minipass": {
-                      "version": "7.1.3"
-                    }
-                  }
-                },
-                "yallist": {
-                  "version": "5.0.0",
-                  "resolved": "https://registry.npmjs.org/yallist/-/yallist-5.0.0.tgz",
-                  "overridden": false
-                }
-              }
-            }
-          }
-        },
-        "onnxruntime-web": {
-          "version": "1.22.0-dev.20250409-89f8206ba4",
-          "resolved": "https://registry.npmjs.org/onnxruntime-web/-/onnxruntime-web-1.22.0-dev.20250409-89f8206ba4.tgz",
-          "overridden": false,
-          "dependencies": {
-            "flatbuffers": {
-              "version": "25.9.23",
-              "resolved": "https://registry.npmjs.org/flatbuffers/-/flatbuffers-25.9.23.tgz",
-              "overridden": false
-            },
-            "guid-typescript": {
-              "version": "1.0.9",
-              "resolved": "https://registry.npmjs.org/guid-typescript/-/guid-typescript-1.0.9.tgz",
-              "overridden": false
-            },
-            "long": {
-              "version": "5.3.2",
-              "resolved": "https://registry.npmjs.org/long/-/long-5.3.2.tgz",
-              "overridden": false
-            },
-            "onnxruntime-common": {
-              "version": "1.22.0-dev.20250409-89f8206ba4",
-              "resolved": "https://registry.npmjs.org/onnxruntime-common/-/onnxruntime-common-1.22.0-dev.20250409-89f8206ba4.tgz",
-              "overridden": false
-            },
-            "platform": {
-              "version": "1.3.6",
-              "resolved": "https://registry.npmjs.org/platform/-/platform-1.3.6.tgz",
-              "overridden": false
-            },
-            "protobufjs": {
-              "version": "7.5.4",
-              "resolved": "https://registry.npmjs.org/protobufjs/-/protobufjs-7.5.4.tgz",
-              "overridden": false,
-              "dependencies": {
-                "@protobufjs/aspromise": {
-                  "version": "1.1.2",
-                  "resolved": "https://registry.npmjs.org/@protobufjs/aspromise/-/aspromise-1.1.2.tgz",
-                  "overridden": false
-                },
-                "@protobufjs/base64": {
-                  "version": "1.1.2",
-                  "resolved": "https://registry.npmjs.org/@protobufjs/base64/-/base64-1.1.2.tgz",
-                  "overridden": false
-                },
-                "@protobufjs/codegen": {
-                  "version": "2.0.4",
-                  "resolved": "https://registry.npmjs.org/@protobufjs/codegen/-/codegen-2.0.4.tgz",
-                  "overridden": false
-                },
-                "@protobufjs/eventemitter": {
-                  "version": "1.1.0",
-                  "resolved": "https://registry.npmjs.org/@protobufjs/eventemitter/-/eventemitter-1.1.0.tgz",
-                  "overridden": false
-                },
-                "@protobufjs/fetch": {
-                  "version": "1.1.0",
-                  "resolved": "https://registry.npmjs.org/@protobufjs/fetch/-/fetch-1.1.0.tgz",
-                  "overridden": false,
-                  "dependencies": {
-                    "@protobufjs/aspromise": {
-                      "version": "1.1.2"
-                    },
-                    "@protobufjs/inquire": {
-                      "version": "1.1.0"
-                    }
-                  }
-                },
-                "@protobufjs/float": {
-                  "version": "1.0.2",
-                  "resolved": "https://registry.npmjs.org/@protobufjs/float/-/float-1.0.2.tgz",
-                  "overridden": false
-                },
-                "@protobufjs/inquire": {
-                  "version": "1.1.0",
-                  "resolved": "https://registry.npmjs.org/@protobufjs/inquire/-/inquire-1.1.0.tgz",
-                  "overridden": false
-                },
-                "@protobufjs/path": {
-                  "version": "1.1.2",
-                  "resolved": "https://registry.npmjs.org/@protobufjs/path/-/path-1.1.2.tgz",
-                  "overridden": false
-                },
-                "@protobufjs/pool": {
-                  "version": "1.1.0",
-                  "resolved": "https://registry.npmjs.org/@protobufjs/pool/-/pool-1.1.0.tgz",
-                  "overridden": false
-                },
-                "@protobufjs/utf8": {
-                  "version": "1.1.0",
-                  "resolved": "https://registry.npmjs.org/@protobufjs/utf8/-/utf8-1.1.0.tgz",
-                  "overridden": false
-                },
-                "@types/node": {
-                  "version": "25.3.0",
-                  "resolved": "https://registry.npmjs.org/@types/node/-/node-25.3.0.tgz",
-                  "overridden": false,
-                  "dependencies": {
-                    "undici-types": {
-                      "version": "7.18.2",
-                      "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-7.18.2.tgz",
-                      "overridden": false
-                    }
-                  }
-                },
-                "long": {
-                  "version": "5.3.2"
-                }
-              }
-            }
-          }
-        },
-        "sharp": {
-          "version": "0.34.5",
-          "resolved": "https://registry.npmjs.org/sharp/-/sharp-0.34.5.tgz",
-          "overridden": false,
-          "dependencies": {
-            "@img/colour": {
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-              "resolved": "https://registry.npmjs.org/@img/colour/-/colour-1.0.0.tgz",
-              "overridden": false
-            },
-            "@img/sharp-darwin-arm64": {},
-            "@img/sharp-darwin-x64": {},
-            "@img/sharp-libvips-darwin-arm64": {},
-            "@img/sharp-libvips-darwin-x64": {},
-            "@img/sharp-libvips-linux-arm": {},
-            "@img/sharp-libvips-linux-arm64": {},
-            "@img/sharp-libvips-linux-ppc64": {},
-            "@img/sharp-libvips-linux-riscv64": {},
-            "@img/sharp-libvips-linux-s390x": {},
-            "@img/sharp-libvips-linux-x64": {
-              "version": "1.2.4",
-              "resolved": "https://registry.npmjs.org/@img/sharp-libvips-linux-x64/-/sharp-libvips-linux-x64-1.2.4.tgz",
-              "overridden": false
-            },
-            "@img/sharp-libvips-linuxmusl-arm64": {},
-            "@img/sharp-libvips-linuxmusl-x64": {
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-              "overridden": false
-            },
-            "@img/sharp-linux-arm": {},
-            "@img/sharp-linux-arm64": {},
-            "@img/sharp-linux-ppc64": {},
-            "@img/sharp-linux-riscv64": {},
-            "@img/sharp-linux-s390x": {},
-            "@img/sharp-linux-x64": {
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-              "resolved": "https://registry.npmjs.org/@img/sharp-linux-x64/-/sharp-linux-x64-0.34.5.tgz",
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-                "@img/sharp-libvips-linux-x64": {
-                  "version": "1.2.4"
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-              }
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-            "@img/sharp-linuxmusl-arm64": {},
-            "@img/sharp-linuxmusl-x64": {
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-                  "version": "1.2.4"
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-              }
-            },
-            "@img/sharp-wasm32": {},
-            "@img/sharp-win32-arm64": {},
-            "@img/sharp-win32-ia32": {},
-            "@img/sharp-win32-x64": {},
-            "detect-libc": {
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-          }
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-    },
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-        "@hono/node-server": {
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-              "resolved": "https://registry.npmjs.org/rc/-/rc-1.2.8.tgz",
-              "overridden": false,
-              "dependencies": {
-                "deep-extend": {
-                  "version": "0.6.0",
-                  "resolved": "https://registry.npmjs.org/deep-extend/-/deep-extend-0.6.0.tgz",
-                  "overridden": false
-                },
-                "ini": {
-                  "version": "1.3.8",
-                  "resolved": "https://registry.npmjs.org/ini/-/ini-1.3.8.tgz",
-                  "overridden": false
-                },
-                "minimist": {
-                  "version": "1.2.8"
-                },
-                "strip-json-comments": {
-                  "version": "2.0.1",
-                  "resolved": "https://registry.npmjs.org/strip-json-comments/-/strip-json-comments-2.0.1.tgz",
-                  "overridden": false
-                }
-              }
-            },
-            "simple-get": {
-              "version": "4.0.1",
-              "resolved": "https://registry.npmjs.org/simple-get/-/simple-get-4.0.1.tgz",
-              "overridden": false,
-              "dependencies": {
-                "decompress-response": {
-                  "version": "6.0.0",
-                  "resolved": "https://registry.npmjs.org/decompress-response/-/decompress-response-6.0.0.tgz",
-                  "overridden": false,
-                  "dependencies": {
-                    "mimic-response": {
-                      "version": "3.1.0",
-                      "resolved": "https://registry.npmjs.org/mimic-response/-/mimic-response-3.1.0.tgz",
-                      "overridden": false
-                    }
-                  }
-                },
-                "once": {
-                  "version": "1.4.0"
-                },
-                "simple-concat": {
-                  "version": "1.0.1",
-                  "resolved": "https://registry.npmjs.org/simple-concat/-/simple-concat-1.0.1.tgz",
-                  "overridden": false
-                }
-              }
-            },
-            "tar-fs": {
-              "version": "2.1.4",
-              "resolved": "https://registry.npmjs.org/tar-fs/-/tar-fs-2.1.4.tgz",
-              "overridden": false,
-              "dependencies": {
-                "chownr": {
-                  "version": "1.1.4",
-                  "resolved": "https://registry.npmjs.org/chownr/-/chownr-1.1.4.tgz",
-                  "overridden": false
-                },
-                "mkdirp-classic": {
-                  "version": "0.5.3"
-                },
-                "pump": {
-                  "version": "3.0.3"
-                },
-                "tar-stream": {
-                  "version": "2.2.0",
-                  "resolved": "https://registry.npmjs.org/tar-stream/-/tar-stream-2.2.0.tgz",
-                  "overridden": false,
-                  "dependencies": {
-                    "bl": {
-                      "version": "4.1.0",
-                      "resolved": "https://registry.npmjs.org/bl/-/bl-4.1.0.tgz",
-                      "overridden": false,
-                      "dependencies": {
-                        "buffer": {
-                          "version": "5.7.1",
-                          "resolved": "https://registry.npmjs.org/buffer/-/buffer-5.7.1.tgz",
-                          "overridden": false,
-                          "dependencies": {
-                            "base64-js": {
-                              "version": "1.5.1",
-                              "resolved": "https://registry.npmjs.org/base64-js/-/base64-js-1.5.1.tgz",
-                              "overridden": false
-                            },
-                            "ieee754": {
-                              "version": "1.2.1",
-                              "resolved": "https://registry.npmjs.org/ieee754/-/ieee754-1.2.1.tgz",
-                              "overridden": false
-                            }
-                          }
-                        },
-                        "inherits": {
-                          "version": "2.0.4"
-                        },
-                        "readable-stream": {
-                          "version": "3.6.2"
-                        }
-                      }
-                    },
-                    "end-of-stream": {
-                      "version": "1.4.5"
-                    },
-                    "fs-constants": {
-                      "version": "1.0.0",
-                      "resolved": "https://registry.npmjs.org/fs-constants/-/fs-constants-1.0.0.tgz",
-                      "overridden": false
-                    },
-                    "inherits": {
-                      "version": "2.0.4"
-                    },
-                    "readable-stream": {
-                      "version": "3.6.2",
-                      "resolved": "https://registry.npmjs.org/readable-stream/-/readable-stream-3.6.2.tgz",
-                      "overridden": false,
-                      "dependencies": {
-                        "inherits": {
-                          "version": "2.0.4"
-                        },
-                        "string_decoder": {
-                          "version": "1.3.0",
-                          "resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-1.3.0.tgz",
-                          "overridden": false,
-                          "dependencies": {
-                            "safe-buffer": {
-                              "version": "5.2.1"
-                            }
-                          }
-                        },
-                        "util-deprecate": {
-                          "version": "1.0.2",
-                          "resolved": "https://registry.npmjs.org/util-deprecate/-/util-deprecate-1.0.2.tgz",
-                          "overridden": false
-                        }
-                      }
-                    }
-                  }
-                }
-              }
-            },
-            "tunnel-agent": {
-              "version": "0.6.0",
-              "resolved": "https://registry.npmjs.org/tunnel-agent/-/tunnel-agent-0.6.0.tgz",
-              "overridden": false,
-              "dependencies": {
-                "safe-buffer": {
-                  "version": "5.2.1",
-                  "resolved": "https://registry.npmjs.org/safe-buffer/-/safe-buffer-5.2.1.tgz",
-                  "overridden": false
-                }
-              }
-            }
-          }
-        }
-      }
-    },
-    "commander": {
-      "version": "14.0.3",
-      "resolved": "https://registry.npmjs.org/commander/-/commander-14.0.3.tgz",
-      "overridden": false
-    },
-    "web-tree-sitter": {
-      "version": "0.26.5",
-      "resolved": "https://registry.npmjs.org/web-tree-sitter/-/web-tree-sitter-0.26.5.tgz",
-      "overridden": false
-    }
-  },
-  "error": {
-    "code": "ELSPROBLEMS",
-    "summary": "invalid: @optave/codegraph-linux-x64-gnu@2.1.0 /home/runner/work/codegraph/codegraph/node_modules/@optave/codegraph-linux-x64-gnu",
-    "detail": ""
-  }
-}
diff --git a/generated/DEPENDENCIES.md b/generated/DEPENDENCIES.md
deleted file mode 100644
index 6a773345..00000000
--- a/generated/DEPENDENCIES.md
+++ /dev/null
@@ -1,315 +0,0 @@
-# Dependencies
-
-```
-@optave/codegraph@2.0.0 h:\Vscode\codegraph\.claude\worktrees\dogfood-2.1.0
-+-- @huggingface/transformers@3.8.1
-| +-- @huggingface/jinja@0.5.5
-| +-- onnxruntime-node@1.21.0
-| | +-- global-agent@3.0.0
-| | | +-- boolean@3.2.0
-| | | +-- es6-error@4.1.1
-| | | +-- matcher@3.0.0
-| | | | `-- escape-string-regexp@4.0.0
-| | | +-- roarr@2.15.4
-| | | | +-- boolean@3.2.0 deduped
-| | | | +-- detect-node@2.1.0
-| | | | +-- globalthis@1.0.4
-| | | | | +-- define-properties@1.2.1
-| | | | | | +-- define-data-property@1.1.4
-| | | | | | | +-- es-define-property@1.0.1 deduped
-| | | | | | | +-- es-errors@1.3.0 deduped
-| | | | | | | `-- gopd@1.2.0 deduped
-| | | | | | +-- has-property-descriptors@1.0.2
-| | | | | | | `-- es-define-property@1.0.1 deduped
-| | | | | | `-- object-keys@1.1.1
-| | | | | `-- gopd@1.2.0
-| | | | +-- json-stringify-safe@5.0.1
-| | | | +-- semver-compare@1.0.0
-| | | | `-- sprintf-js@1.1.3
-| | | +-- semver@7.7.4 deduped
-| | | `-- serialize-error@7.0.1
-| | |   `-- type-fest@0.13.1
-| | +-- onnxruntime-common@1.21.0
-| | `-- tar@7.5.9
-| |   +-- @isaacs/fs-minipass@4.0.1
-| |   | `-- minipass@7.1.3 deduped
-| |   +-- chownr@3.0.0
-| |   +-- minipass@7.1.3
-| |   +-- minizlib@3.1.0
-| |   | `-- minipass@7.1.3 deduped
-| |   `-- yallist@5.0.0
-| +-- onnxruntime-web@1.22.0-dev.20250409-89f8206ba4
-| | +-- flatbuffers@25.9.23
-| | +-- guid-typescript@1.0.9
-| | +-- long@5.3.2
-| | +-- onnxruntime-common@1.22.0-dev.20250409-89f8206ba4
-| | +-- platform@1.3.6
-| | `-- protobufjs@7.5.4
-| |   +-- @protobufjs/aspromise@1.1.2
-| |   +-- @protobufjs/base64@1.1.2
-| |   +-- @protobufjs/codegen@2.0.4
-| |   +-- @protobufjs/eventemitter@1.1.0
-| |   +-- @protobufjs/fetch@1.1.0
-| |   | +-- @protobufjs/aspromise@1.1.2 deduped
-| |   | `-- @protobufjs/inquire@1.1.0 deduped
-| |   +-- @protobufjs/float@1.0.2
-| |   +-- @protobufjs/inquire@1.1.0
-| |   +-- @protobufjs/path@1.1.2
-| |   +-- @protobufjs/pool@1.1.0
-| |   +-- @protobufjs/utf8@1.1.0
-| |   +-- @types/node@25.3.0
-| |   | `-- undici-types@7.18.2
-| |   `-- long@5.3.2 deduped
-| `-- sharp@0.34.5
-|   +-- @img/colour@1.0.0
-|   +-- @img/sharp-darwin-arm64@0.34.5
-|   | `-- @img/sharp-libvips-darwin-arm64@1.2.4 deduped
-|   +-- @img/sharp-darwin-x64@0.34.5
-|   | `-- @img/sharp-libvips-darwin-x64@1.2.4 deduped
-|   +-- @img/sharp-libvips-darwin-arm64@1.2.4
-|   +-- @img/sharp-libvips-darwin-x64@1.2.4
-|   +-- @img/sharp-libvips-linux-arm@1.2.4
-|   +-- @img/sharp-libvips-linux-arm64@1.2.4
-|   +-- @img/sharp-libvips-linux-ppc64@1.2.4
-|   +-- @img/sharp-libvips-linux-riscv64@1.2.4
-|   +-- @img/sharp-libvips-linux-s390x@1.2.4
-|   +-- @img/sharp-libvips-linux-x64@1.2.4
-|   +-- @img/sharp-libvips-linuxmusl-arm64@1.2.4
-|   +-- @img/sharp-libvips-linuxmusl-x64@1.2.4
-|   +-- @img/sharp-linux-arm@0.34.5
-|   | `-- @img/sharp-libvips-linux-arm@1.2.4 deduped
-|   +-- @img/sharp-linux-arm64@0.34.5
-|   | `-- @img/sharp-libvips-linux-arm64@1.2.4 deduped
-|   +-- @img/sharp-linux-ppc64@0.34.5
-|   | `-- @img/sharp-libvips-linux-ppc64@1.2.4 deduped
-|   +-- @img/sharp-linux-riscv64@0.34.5
-|   | `-- @img/sharp-libvips-linux-riscv64@1.2.4 deduped
-|   +-- @img/sharp-linux-s390x@0.34.5
-|   | `-- @img/sharp-libvips-linux-s390x@1.2.4 deduped
-|   +-- @img/sharp-linux-x64@0.34.5
-|   | `-- @img/sharp-libvips-linux-x64@1.2.4 deduped
-|   +-- @img/sharp-linuxmusl-arm64@0.34.5
-|   | `-- @img/sharp-libvips-linuxmusl-arm64@1.2.4 deduped
-|   +-- @img/sharp-linuxmusl-x64@0.34.5
-|   | `-- @img/sharp-libvips-linuxmusl-x64@1.2.4 deduped
-|   +-- @img/sharp-wasm32@0.34.5
-|   | `-- @emnapi/runtime@1.8.1
-|   |   `-- tslib@2.8.1
-|   +-- @img/sharp-win32-arm64@0.34.5
-|   +-- @img/sharp-win32-ia32@0.34.5
-|   +-- @img/sharp-win32-x64@0.34.5
-|   +-- detect-libc@2.1.2
-|   `-- semver@7.7.4
-+-- @modelcontextprotocol/sdk@1.26.0
-| +-- UNMET OPTIONAL DEPENDENCY @cfworker/json-schema@^4.1.1
-| +-- @hono/node-server@1.19.9
-| | `-- hono@4.12.0 deduped
-| +-- ajv-formats@3.0.1
-| | `-- ajv@8.18.0 deduped
-| +-- ajv@8.18.0
-| | +-- fast-deep-equal@3.1.3
-| | +-- fast-uri@3.1.0
-| | +-- json-schema-traverse@1.0.0
-| | `-- require-from-string@2.0.2
-| +-- content-type@1.0.5
-| +-- cors@2.8.6
-| | +-- object-assign@4.1.1
-| | `-- vary@1.1.2
-| +-- cross-spawn@7.0.6
-| | +-- path-key@3.1.1
-| | +-- shebang-command@2.0.0
-| | | `-- shebang-regex@3.0.0
-| | `-- which@2.0.2
-| |   `-- isexe@2.0.0
-| +-- eventsource-parser@3.0.6
-| +-- eventsource@3.0.7
-| | `-- eventsource-parser@3.0.6 deduped
-| +-- express-rate-limit@8.2.1
-| | +-- express@5.2.1 deduped
-| | `-- ip-address@10.0.1
-| +-- express@5.2.1
-| | +-- accepts@2.0.0
-| | | +-- mime-types@3.0.2 deduped
-| | | `-- negotiator@1.0.0
-| | +-- body-parser@2.2.2
-| | | +-- bytes@3.1.2 deduped
-| | | +-- content-type@1.0.5 deduped
-| | | +-- debug@4.4.3 deduped
-| | | +-- http-errors@2.0.1 deduped
-| | | +-- iconv-lite@0.7.2 deduped
-| | | +-- on-finished@2.4.1 deduped
-| | | +-- qs@6.15.0 deduped
-| | | +-- raw-body@3.0.2 deduped
-| | | `-- type-is@2.0.1 deduped
-| | +-- content-disposition@1.0.1
-| | +-- content-type@1.0.5 deduped
-| | +-- cookie-signature@1.2.2
-| | +-- cookie@0.7.2
-| | +-- debug@4.4.3
-| | | `-- ms@2.1.3
-| | +-- depd@2.0.0
-| | +-- encodeurl@2.0.0
-| | +-- escape-html@1.0.3
-| | +-- etag@1.8.1
-| | +-- finalhandler@2.1.1
-| | | +-- debug@4.4.3 deduped
-| | | +-- encodeurl@2.0.0 deduped
-| | | +-- escape-html@1.0.3 deduped
-| | | +-- on-finished@2.4.1 deduped
-| | | +-- parseurl@1.3.3 deduped
-| | | `-- statuses@2.0.2 deduped
-| | +-- fresh@2.0.0
-| | +-- http-errors@2.0.1
-| | | +-- depd@2.0.0 deduped
-| | | +-- inherits@2.0.4
-| | | +-- setprototypeof@1.2.0
-| | | +-- statuses@2.0.2 deduped
-| | | `-- toidentifier@1.0.1
-| | +-- merge-descriptors@2.0.0
-| | +-- mime-types@3.0.2
-| | | `-- mime-db@1.54.0
-| | +-- on-finished@2.4.1
-| | | `-- ee-first@1.1.1
-| | +-- once@1.4.0
-| | | `-- wrappy@1.0.2
-| | +-- parseurl@1.3.3
-| | +-- proxy-addr@2.0.7
-| | | +-- forwarded@0.2.0
-| | | `-- ipaddr.js@1.9.1
-| | +-- qs@6.15.0
-| | | `-- side-channel@1.1.0
-| | |   +-- es-errors@1.3.0
-| | |   +-- object-inspect@1.13.4
-| | |   +-- side-channel-list@1.0.0
-| | |   | +-- es-errors@1.3.0 deduped
-| | |   | `-- object-inspect@1.13.4 deduped
-| | |   +-- side-channel-map@1.0.1
-| | |   | +-- call-bound@1.0.4
-| | |   | | +-- call-bind-apply-helpers@1.0.2
-| | |   | | | +-- es-errors@1.3.0 deduped
-| | |   | | | `-- function-bind@1.1.2 deduped
-| | |   | | `-- get-intrinsic@1.3.0 deduped
-| | |   | +-- es-errors@1.3.0 deduped
-| | |   | +-- get-intrinsic@1.3.0
-| | |   | | +-- call-bind-apply-helpers@1.0.2 deduped
-| | |   | | +-- es-define-property@1.0.1
-| | |   | | +-- es-errors@1.3.0 deduped
-| | |   | | +-- es-object-atoms@1.1.1
-| | |   | | | `-- es-errors@1.3.0 deduped
-| | |   | | +-- function-bind@1.1.2
-| | |   | | +-- get-proto@1.0.1
-| | |   | | | +-- dunder-proto@1.0.1
-| | |   | | | | +-- call-bind-apply-helpers@1.0.2 deduped
-| | |   | | | | +-- es-errors@1.3.0 deduped
-| | |   | | | | `-- gopd@1.2.0 deduped
-| | |   | | | `-- es-object-atoms@1.1.1 deduped
-| | |   | | +-- gopd@1.2.0 deduped
-| | |   | | +-- has-symbols@1.1.0
-| | |   | | +-- hasown@2.0.2
-| | |   | | | `-- function-bind@1.1.2 deduped
-| | |   | | `-- math-intrinsics@1.1.0
-| | |   | `-- object-inspect@1.13.4 deduped
-| | |   `-- side-channel-weakmap@1.0.2
-| | |     +-- call-bound@1.0.4 deduped
-| | |     +-- es-errors@1.3.0 deduped
-| | |     +-- get-intrinsic@1.3.0 deduped
-| | |     +-- object-inspect@1.13.4 deduped
-| | |     `-- side-channel-map@1.0.1 deduped
-| | +-- range-parser@1.2.1
-| | +-- router@2.2.0
-| | | +-- debug@4.4.3 deduped
-| | | +-- depd@2.0.0 deduped
-| | | +-- is-promise@4.0.0
-| | | +-- parseurl@1.3.3 deduped
-| | | `-- path-to-regexp@8.3.0
-| | +-- send@1.2.1
-| | | +-- debug@4.4.3 deduped
-| | | +-- encodeurl@2.0.0 deduped
-| | | +-- escape-html@1.0.3 deduped
-| | | +-- etag@1.8.1 deduped
-| | | +-- fresh@2.0.0 deduped
-| | | +-- http-errors@2.0.1 deduped
-| | | +-- mime-types@3.0.2 deduped
-| | | +-- ms@2.1.3 deduped
-| | | +-- on-finished@2.4.1 deduped
-| | | +-- range-parser@1.2.1 deduped
-| | | `-- statuses@2.0.2 deduped
-| | +-- serve-static@2.2.1
-| | | +-- encodeurl@2.0.0 deduped
-| | | +-- escape-html@1.0.3 deduped
-| | | +-- parseurl@1.3.3 deduped
-| | | `-- send@1.2.1 deduped
-| | +-- statuses@2.0.2
-| | +-- type-is@2.0.1
-| | | +-- content-type@1.0.5 deduped
-| | | +-- media-typer@1.1.0
-| | | `-- mime-types@3.0.2 deduped
-| | `-- vary@1.1.2 deduped
-| +-- hono@4.12.0
-| +-- jose@6.1.3
-| +-- json-schema-typed@8.0.2
-| +-- pkce-challenge@5.0.1
-| +-- raw-body@3.0.2
-| | +-- bytes@3.1.2
-| | +-- http-errors@2.0.1 deduped
-| | +-- iconv-lite@0.7.2
-| | | `-- safer-buffer@2.1.2
-| | `-- unpipe@1.0.0
-| +-- zod-to-json-schema@3.25.1
-| | `-- zod@4.3.6 deduped
-| `-- zod@4.3.6
-+-- @optave/codegraph-darwin-arm64@2.0.0
-+-- @optave/codegraph-darwin-x64@2.0.0
-+-- @optave/codegraph-linux-x64-gnu@2.0.0
-+-- @optave/codegraph-win32-x64-msvc@2.0.0
-+-- better-sqlite3@12.6.2
-| +-- bindings@1.5.0
-| | `-- file-uri-to-path@1.0.0
-| `-- prebuild-install@7.1.3
-|   +-- detect-libc@2.1.2 deduped
-|   +-- expand-template@2.0.3
-|   +-- github-from-package@0.0.0
-|   +-- minimist@1.2.8
-|   +-- mkdirp-classic@0.5.3
-|   +-- napi-build-utils@2.0.0
-|   +-- node-abi@3.87.0
-|   | `-- semver@7.7.4 deduped
-|   +-- pump@3.0.3
-|   | +-- end-of-stream@1.4.5
-|   | | `-- once@1.4.0 deduped
-|   | `-- once@1.4.0 deduped
-|   +-- rc@1.2.8
-|   | +-- deep-extend@0.6.0
-|   | +-- ini@1.3.8
-|   | +-- minimist@1.2.8 deduped
-|   | `-- strip-json-comments@2.0.1
-|   +-- simple-get@4.0.1
-|   | +-- decompress-response@6.0.0
-|   | | `-- mimic-response@3.1.0
-|   | +-- once@1.4.0 deduped
-|   | `-- simple-concat@1.0.1
-|   +-- tar-fs@2.1.4
-|   | +-- chownr@1.1.4
-|   | +-- mkdirp-classic@0.5.3 deduped
-|   | +-- pump@3.0.3 deduped
-|   | `-- tar-stream@2.2.0
-|   |   +-- bl@4.1.0
-|   |   | +-- buffer@5.7.1
-|   |   | | +-- base64-js@1.5.1
-|   |   | | `-- ieee754@1.2.1
-|   |   | +-- inherits@2.0.4 deduped
-|   |   | `-- readable-stream@3.6.2 deduped
-|   |   +-- end-of-stream@1.4.5 deduped
-|   |   +-- fs-constants@1.0.0
-|   |   +-- inherits@2.0.4 deduped
-|   |   `-- readable-stream@3.6.2
-|   |     +-- inherits@2.0.4 deduped
-|   |     +-- string_decoder@1.3.0
-|   |     | `-- safe-buffer@5.2.1 deduped
-|   |     `-- util-deprecate@1.0.2
-|   `-- tunnel-agent@0.6.0
-|     `-- safe-buffer@5.2.1
-+-- commander@14.0.3
-`-- web-tree-sitter@0.26.5
-
-```
diff --git a/scripts/gen-deps.cjs b/scripts/gen-deps.cjs
index 16e1ca1b..32072004 100644
--- a/scripts/gen-deps.cjs
+++ b/scripts/gen-deps.cjs
@@ -1,18 +1,19 @@
 const { execSync } = require('child_process');
 const fs = require('fs');
+const path = require('path');
+
+const outFile = path.join('generated', 'DEPENDENCIES.md');
+fs.mkdirSync(path.dirname(outFile), { recursive: true });
 
 try {
   const tree = execSync('npm ls --all --omit=dev', { encoding: 'utf8' });
-  fs.writeFileSync(
-    'DEPENDENCIES.md',
-    '# Dependencies\n\n```\n' + tree + '```\n',
-  );
+  fs.writeFileSync(outFile, '# Dependencies\n\n```\n' + tree + '```\n');
 } catch (err) {
   // npm ls exits non-zero on ELSPROBLEMS (version mismatches in optional deps).
   // If stdout still has content, write it; otherwise skip silently.
   if (err.stdout) {
     fs.writeFileSync(
-      'DEPENDENCIES.md',
+      outFile,
       '# Dependencies\n\n```\n' + err.stdout + '```\n',
     );
   } else {