@sppg2001/atomize 5.1.1 → 5.1.3

package/README.md

@@ -1,11 +1,23 @@
 # Atomize CLI
 
-Atomize CLI turns stories into consistent child tasks using reusable YAML templates. It supports template validation, safe previews, confirmed task generation, connection profile management, template catalog operations, and CI/CD automation.
+**Break down stories, build up velocity.**
 
-Atomize is designed around platform adapters. Today, connected generation supports Azure DevOps. Mock is available for offline testing.
+Atomize turns Stories into consistent child Tasks using reusable YAML Templates. Capture your team's task breakdown once, then validate, preview, and reuse it from your terminal or CI/CD pipeline.
+
+- Try built-in Templates offline with Mock Stories.
+- Customize task titles, descriptions, conditions, dependencies, and estimation rules in YAML.
+- Reuse Templates and Mixins from built-in, user, and project Catalogs.
+- Draft and improve Templates with your GitHub Copilot account.
+- Preview real Azure DevOps Stories before confirming task creation.
+
+Connected generation currently supports **Azure DevOps**. Offline Validation and Mock Preview require no platform account or Connection Profile.
+
+[Website and documentation](https://atomize-docs.pages.dev/) · [CLI quickstart](https://atomize-docs.pages.dev/getting-started/cli/) · [Source and issues](https://github.com/Simao-Pereira-Gomes/atomize)
 
 ## Install
 
+Requires [Node.js](https://nodejs.org/) **22 or later** and npm.
+
 ```bash
 npm install -g @sppg2001/atomize
 ```
@@ -25,21 +37,28 @@ npx @sppg2001/atomize --help
 
 ## Quick Start
 
-Try Atomize without credentials:
+### Try it offline
+
+The `backend-api` Template ships with the CLI. Validate it, then preview a task breakdown using a Mock Story:
 
 ```bash
 atomize validate template:backend-api
-atomize generate template:backend-api --platform mock
+atomize preview template:backend-api \
+  --mock-story '{"id":"123","title":"Add password reset","estimation":8}'
 ```
 
-Connect Azure DevOps:
+The preview returns three Tasks: define API behavior, implement the change, and verify it. The example Template converts the Story Estimate of 8 into a 32-hour budget and splits it 20% / 50% / 30%. Change the title or estimate and run it again to see the breakdown change. No Work Items are created.
+
+### Connect Azure DevOps
+
+Add a Connection Profile using an Azure DevOps PAT with **Work Items read/write** access:
 
 ```bash
 atomize auth add work-ado
 atomize auth test work-ado
 ```
 
-Preview and then create tasks:
+Preview real Stories, then create Tasks after reviewing the plan:
 
 ```bash
 # Dry run, no tasks created
@@ -49,6 +68,8 @@ atomize generate template:backend-api --profile work-ado
 atomize generate template:backend-api --profile work-ado --execute
 ```
 
+Use `--story 123 456` to select specific Stories. See the [Auth Guide](https://atomize-docs.pages.dev/connections/profiles/) for PAT permissions, credential storage, and profile setup.
+
 ## Safety Model
 
 `atomize generate` is a dry run by default. It calculates the task plan but does not create tasks.
@@ -103,6 +124,20 @@ atomize fields list --type Task
 atomize queries list
 ```
 
+## AI-Assisted Authoring
+
+Use your signed-in GitHub Copilot account to draft a Template from prose or review a proposed improvement to an existing one:
+
+```bash
+atomize template create --ai
+atomize template improve template:backend-api
+
+# Draft with your team's written process as reference material
+atomize template create --ai --reference docs/how-we-work.md
+```
+
+AI authoring uses a separate Copilot Session; it does not require an Azure DevOps Connection Profile. You can explicitly add project context with `--ground --profile work-ado`. See [AI authoring](https://atomize-docs.pages.dev/cli/ai/) for sign-in, Reference Documents, and review workflows.
+
 ## CI/CD
 
 Validate first, then run live generation with explicit acknowledgement:
@@ -134,22 +169,23 @@ Validate first, then run live generation with explicit acknowledgement:
       --output report.json
 ```
 
-## VS Code Extension
+## Desktop and Editor Workflows
 
-Prefer an editor workflow? Atomize also has a VS Code extension for YAML authoring, validation, mock/live preview, profile management, catalog browsing, and confirmed generation.
+- **[Atomize Studio](https://github.com/Simao-Pereira-Gomes/atomize/blob/main/docs/Atomize-Studio.md)** is a standalone desktop app for visual Template authoring, Catalog management, and confirmed task generation. Download an installer via [Studio Releases](https://github.com/Simao-Pereira-Gomes/atomize/blob/main/docs/Studio-Releases.md).
+- **[VS Code extension](https://atomize-docs.pages.dev/getting-started/vscode/)** provides YAML completions, schema hovers, diagnostics, Mock and Live Preview, and confirmed generation in your editor.
 
-See the [VS Code Extension Guide](https://github.com/Simao-Pereira-Gomes/atomize/blob/main/docs/VS-Code-Extension.md).
+The CLI and Studio share Connection Profile metadata and compatible OS-keyring-backed tokens. VS Code manages its own profiles. See the [Auth Guide](https://atomize-docs.pages.dev/connections/profiles/#shared-between-the-cli-and-atomize-studio) for details.
 
 ## Documentation
 
-- [Product README](https://github.com/Simao-Pereira-Gomes/atomize#readme) - VS Code-first onboarding and product overview
-- [Documentation Index](https://github.com/Simao-Pereira-Gomes/atomize/blob/main/docs/README.md)
-- [Workflows](https://github.com/Simao-Pereira-Gomes/atomize/blob/main/docs/Workflows.md)
-- [CLI Reference](https://github.com/Simao-Pereira-Gomes/atomize/blob/main/docs/Cli-Reference.md)
-- [Template Creation](https://github.com/Simao-Pereira-Gomes/atomize/blob/main/docs/Template-Creation.md)
-- [Template Reference](https://github.com/Simao-Pereira-Gomes/atomize/blob/main/docs/Template-Reference.md)
-- [Auth Guide](https://github.com/Simao-Pereira-Gomes/atomize/blob/main/docs/Auth-Guide.md)
-- [Platform Guide](https://github.com/Simao-Pereira-Gomes/atomize/blob/main/docs/Platform-Guide.md)
+- [Website and Documentation](https://atomize-docs.pages.dev/)
+- [Workflows](https://atomize-docs.pages.dev/workflows/)
+- [CLI Reference](https://atomize-docs.pages.dev/cli/reference/)
+- [Template Creation](https://atomize-docs.pages.dev/catalog/create/)
+- [Schema Reference](https://atomize-docs.pages.dev/reference/templates/schema/)
+- [Template Reference](https://atomize-docs.pages.dev/reference/templates/)
+- [Auth Guide](https://atomize-docs.pages.dev/connections/profiles/)
+- [Platform Guide](https://atomize-docs.pages.dev/connections/)
 
 ## License
 

package/dist/cli/index.js

@@ -24217,13 +24217,14 @@ var require_side_channel = __commonJS((exports, module) => {
   };
 });
 
-// ../../node_modules/.bun/qs@6.16.0/node_modules/qs/lib/formats.js
+// ../../node_modules/.bun/qs@6.17.1/node_modules/qs/lib/formats.js
 var require_formats = __commonJS((exports, module) => {
   var replace = String.prototype.replace;
   var percentTwenties = /%20/g;
   var Format = {
     RFC1738: "RFC1738",
-    RFC3986: "RFC3986"
+    RFC3986: "RFC3986",
+    WHATWG: "WHATWG"
   };
   module.exports = {
     default: Format.RFC3986,
@@ -24233,14 +24234,18 @@ var require_formats = __commonJS((exports, module) => {
       },
       RFC3986: function(value) {
         return String(value);
+      },
+      WHATWG: function(value) {
+        return replace.call(value, percentTwenties, "+");
       }
     },
     RFC1738: Format.RFC1738,
-    RFC3986: Format.RFC3986
+    RFC3986: Format.RFC3986,
+    WHATWG: Format.WHATWG
   };
 });
 
-// ../../node_modules/.bun/qs@6.16.0/node_modules/qs/lib/utils.js
+// ../../node_modules/.bun/qs@6.17.1/node_modules/qs/lib/utils.js
 var require_utils = __commonJS((exports, module) => {
   var formats = require_formats();
   var getSideChannel = require_side_channel();
@@ -24261,6 +24266,17 @@ var require_utils = __commonJS((exports, module) => {
   var setMaxIndex = function setMaxIndex2(obj, maxIndex) {
     overflowChannel.set(obj, maxIndex);
   };
+  var conflictChannel = getSideChannel();
+  var markConflict = function markConflict2(obj, maxIndex) {
+    conflictChannel.set(obj, maxIndex);
+    return obj;
+  };
+  var isConflict = function isConflict2(obj) {
+    return conflictChannel.has(obj);
+  };
+  var getConflictIndex = function getConflictIndex2(obj) {
+    return conflictChannel.get(obj);
+  };
   var hexTable = function() {
     var array2 = [];
     for (var i2 = 0;i2 < 256; ++i2) {
@@ -24304,6 +24320,36 @@ var require_utils = __commonJS((exports, module) => {
       obj[key] = value;
     }
   };
+  var maxNumericIndex = function maxNumericIndex2(obj, min) {
+    var max = min;
+    var keys = Object.keys(obj);
+    for (var i2 = 0;i2 < keys.length; ++i2) {
+      var num = parseInt(keys[i2], 10);
+      if (String(num) === keys[i2] && num > max) {
+        max = num;
+      }
+    }
+    return max;
+  };
+  var countElements = function countElements2(arr) {
+    var count = 0;
+    for (var i2 = 0;i2 < arr.length; ++i2) {
+      if (has.call(arr, i2)) {
+        count += 1;
+      }
+    }
+    return count;
+  };
+  var limitedPair = function limitedPair2(first, second, options) {
+    var pair = [first, second];
+    if (options && typeof options.arrayLimit === "number" && pair.length > options.arrayLimit) {
+      if (options.throwOnLimitExceeded) {
+        throw new RangeError("Array limit exceeded. Only " + options.arrayLimit + " element" + (options.arrayLimit === 1 ? "" : "s") + " allowed in an array.");
+      }
+      return markOverflow(arrayToObject(pair, options), 1);
+    }
+    return pair;
+  };
   var merge2 = function merge3(target, source, options) {
     if (!source) {
       return target;
@@ -24311,7 +24357,7 @@ var require_utils = __commonJS((exports, module) => {
     if (typeof source !== "object" && typeof source !== "function") {
       if (isArray(target)) {
         var nextIndex = target.length;
-        if (options && typeof options.arrayLimit === "number" && nextIndex >= options.arrayLimit) {
+        if (options && typeof options.arrayLimit === "number" && countElements(target) >= options.arrayLimit) {
           if (options.throwOnLimitExceeded) {
             throw new RangeError("Array limit exceeded. Only " + options.arrayLimit + " element" + (options.arrayLimit === 1 ? "" : "s") + " allowed in an array.");
           }
@@ -24323,13 +24369,21 @@ var require_utils = __commonJS((exports, module) => {
           var newIndex = getMaxIndex(target) + 1;
           target[newIndex] = source;
           setMaxIndex(target, newIndex);
+        } else if (options && options.strictMerge && isConflict(target)) {
+          var nextConflict = getConflictIndex(target) + 1;
+          if (options.throwOnLimitExceeded && typeof options.arrayLimit === "number" && nextConflict >= options.arrayLimit) {
+            throw new RangeError("Array limit exceeded. Only " + options.arrayLimit + " element" + (options.arrayLimit === 1 ? "" : "s") + " allowed in an array.");
+          }
+          target[nextConflict] = source;
+          markConflict(target, nextConflict);
         } else if (options && options.strictMerge) {
-          return [target, source];
+          var conflict = limitedPair(target, source, options);
+          return isArray(conflict) ? markConflict(conflict, 1) : conflict;
         } else if (options && (options.plainObjects || options.allowPrototypes) || !has.call(Object.prototype, source)) {
           target[source] = true;
         }
       } else {
-        return [target, source];
+        return limitedPair(target, source, options);
       }
       return target;
     }
@@ -24355,6 +24409,9 @@ var require_utils = __commonJS((exports, module) => {
     var mergeTarget = target;
     if (isArray(target) && !isArray(source)) {
       mergeTarget = arrayToObject(target, options);
+      if (isConflict(target)) {
+        markConflict(mergeTarget, target.length - 1);
+      }
     }
     if (isArray(target) && isArray(source)) {
       source.forEach(function(item, i2) {
@@ -24369,7 +24426,7 @@ var require_utils = __commonJS((exports, module) => {
           target[i2] = item;
         }
       });
-      if (options && typeof options.arrayLimit === "number" && target.length > options.arrayLimit) {
+      if (options && typeof options.arrayLimit === "number" && countElements(target) > options.arrayLimit) {
         if (options.throwOnLimitExceeded) {
           throw new RangeError("Array limit exceeded. Only " + options.arrayLimit + " element" + (options.arrayLimit === 1 ? "" : "s") + " allowed in an array.");
         }
@@ -24385,7 +24442,7 @@ var require_utils = __commonJS((exports, module) => {
         setProperty(acc, key, value);
       }
       if (isOverflow(source) && !isOverflow(acc)) {
-        markOverflow(acc, getMaxIndex(source));
+        markOverflow(acc, maxNumericIndex(acc, getMaxIndex(source)));
       }
       if (isOverflow(acc)) {
         var keyNum = parseInt(key, 10);
@@ -24393,6 +24450,12 @@ var require_utils = __commonJS((exports, module) => {
           setMaxIndex(acc, keyNum);
         }
       }
+      if (isConflict(acc)) {
+        var conflictKey = parseInt(key, 10);
+        if (String(conflictKey) === key && conflictKey > getConflictIndex(acc)) {
+          markConflict(acc, conflictKey);
+        }
+      }
       return acc;
     }, mergeTarget);
   };
@@ -24403,6 +24466,9 @@ var require_utils = __commonJS((exports, module) => {
     }, target);
   };
   var decode3 = function(str, defaultDecoder, charset) {
+    if (typeof str === "string" && str.indexOf("%") === -1) {
+      return str.indexOf("+") === -1 ? str : str.replace(/\+/g, " ");
+    }
     var strWithoutPlus = str.replace(/\+/g, " ");
     if (charset === "iso-8859-1") {
       return strWithoutPlus.replace(/%[0-9a-f]{2}/gi, unescape);
@@ -24413,6 +24479,52 @@ var require_utils = __commonJS((exports, module) => {
       return strWithoutPlus;
     }
   };
+  var hasToPrimitive = typeof Symbol === "function" && typeof Symbol.toPrimitive === "symbol";
+  var arrayJoin = Array.prototype.join;
+  var arrayToString = Array.prototype.toString;
+  var objectToString = Object.prototype.toString;
+  var toCoercible = function toCoercible2(value, joining) {
+    if (!value || typeof value !== "object" && typeof value !== "function") {
+      return value;
+    }
+    if (hasToPrimitive && value[Symbol.toPrimitive] != null) {
+      return value;
+    }
+    if (isArray(value) && value.toString === arrayToString && value.join === arrayJoin) {
+      var ancestors = joining || getSideChannel();
+      if (ancestors.has(value)) {
+        return "";
+      }
+      ancestors.set(value, true);
+      var copy;
+      for (var i2 = 0;i2 < value.length; i2 += 1) {
+        var item = value[i2];
+        var coerced = toCoercible2(item, ancestors);
+        if (!copy && coerced !== item) {
+          copy = [];
+          for (var j2 = 0;j2 < i2; j2 += 1) {
+            copy[j2] = value[j2];
+          }
+        }
+        if (copy) {
+          copy[i2] = coerced;
+        }
+      }
+      ancestors["delete"](value);
+      return copy || value;
+    }
+    if (typeof value.toString === "function") {
+      return value;
+    }
+    var valueOf = value.valueOf;
+    if (typeof valueOf === "function") {
+      var primitive = valueOf.call(value);
+      if (!primitive || typeof primitive !== "object" && typeof primitive !== "function") {
+        return String(primitive);
+      }
+    }
+    return objectToString.call(value);
+  };
   var limit = 1024;
   var encode3 = function encode4(str, defaultEncoder, charset, kind, format) {
     if (str.length === 0) {
@@ -24422,12 +24534,12 @@ var require_utils = __commonJS((exports, module) => {
     if (typeof str === "symbol") {
       string4 = Symbol.prototype.toString.call(str);
     } else if (typeof str !== "string") {
-      string4 = String(str);
+      string4 = String(toCoercible(str));
     }
     if (charset === "iso-8859-1") {
       return escape(string4).replace(/%u[0-9a-f]{4}/gi, function($0) {
         return "%26%23" + parseInt($0.slice(2), 16) + "%3B";
-      });
+      }).replace(/\+/g, "%2B");
     }
     var out = "";
     for (var j2 = 0;j2 < string4.length; j2 += limit) {
@@ -24442,7 +24554,7 @@ var require_utils = __commonJS((exports, module) => {
       var arr = [];
       for (var i2 = 0;i2 < segment.length; ++i2) {
         var c2 = segment.charCodeAt(i2);
-        if (c2 === 45 || c2 === 46 || c2 === 95 || c2 === 126 || c2 >= 48 && c2 <= 57 || c2 >= 65 && c2 <= 90 || c2 >= 97 && c2 <= 122 || format === formats.RFC1738 && (c2 === 40 || c2 === 41)) {
+        if (c2 === 45 || c2 === 46 || c2 === 95 || c2 === 126 && format !== formats.WHATWG || c2 >= 48 && c2 <= 57 || c2 >= 65 && c2 <= 90 || c2 >= 97 && c2 <= 122 || format === formats.RFC1738 && (c2 === 40 || c2 === 41) || format === formats.WHATWG && c2 === 42) {
           arr[arr.length] = segment.charAt(i2);
           continue;
         }
@@ -24458,9 +24570,14 @@ var require_utils = __commonJS((exports, module) => {
           arr[arr.length] = hexTable[224 | c2 >> 12] + hexTable[128 | c2 >> 6 & 63] + hexTable[128 | c2 & 63];
           continue;
         }
-        i2 += 1;
-        c2 = 65536 + ((c2 & 1023) << 10 | segment.charCodeAt(i2) & 1023);
-        arr[arr.length] = hexTable[240 | c2 >> 18] + hexTable[128 | c2 >> 12 & 63] + hexTable[128 | c2 >> 6 & 63] + hexTable[128 | c2 & 63];
+        var next = segment.charCodeAt(i2 + 1);
+        if (c2 <= 56319 && next >= 56320 && next <= 57343) {
+          i2 += 1;
+          c2 = 65536 + ((c2 & 1023) << 10 | next & 1023);
+          arr[arr.length] = hexTable[240 | c2 >> 18] + hexTable[128 | c2 >> 12 & 63] + hexTable[128 | c2 >> 6 & 63] + hexTable[128 | c2 & 63];
+        } else {
+          arr[arr.length] = "%EF%BF%BD";
+        }
       }
       out += arr.join("");
     }
@@ -24539,11 +24656,13 @@ var require_utils = __commonJS((exports, module) => {
     isRegExp,
     markOverflow,
     maybeMap,
-    merge: merge2
+    merge: merge2,
+    setProperty,
+    toCoercible
   };
 });
 
-// ../../node_modules/.bun/qs@6.16.0/node_modules/qs/lib/stringify.js
+// ../../node_modules/.bun/qs@6.17.1/node_modules/qs/lib/stringify.js
 var require_stringify = __commonJS((exports, module) => {
   var getSideChannel = require_side_channel();
   var utils = require_utils();
@@ -24650,20 +24769,20 @@ var require_stringify = __commonJS((exports, module) => {
     if (generateArrayPrefix === "comma" && isArray(obj)) {
       if (encodeValuesOnly && encoder) {
         obj = utils.maybeMap(obj, function(v2) {
-          return v2 == null ? v2 : encoder(v2);
+          return v2 == null ? v2 : encoder(v2, defaults.encoder, charset, "value", format);
         });
       }
-      objKeys = [{ value: obj.length > 0 ? obj.join(",") || null : undefined }];
+      objKeys = [{ value: obj.length > 0 ? utils.toCoercible(obj).join(",") || null : undefined }];
     } else if (isArray(filter)) {
       objKeys = filter;
     } else {
       var keys = Object.keys(obj);
       objKeys = sort ? keys.sort(sort) : keys;
     }
-    var encodedPrefix = encodeDotInKeys ? String(prefix).replace(/\./g, "%2E") : String(prefix);
+    var encodedPrefix = String(prefix);
     var adjustedPrefix = commaRoundTrip && isArray(obj) && obj.length === 1 ? encodedPrefix + "[]" : encodedPrefix;
     if (allowEmptyArrays && isArray(obj) && obj.length === 0 && Object.keys(obj).length === 0) {
-      return adjustedPrefix + "[]";
+      return formatter(encoder && !encodeValuesOnly ? encoder(adjustedPrefix, defaults.encoder, charset, "key", format) : adjustedPrefix) + "[]";
     }
     for (var j2 = 0;j2 < objKeys.length; ++j2) {
       var key = objKeys[j2];
@@ -24710,7 +24829,7 @@ var require_stringify = __commonJS((exports, module) => {
       filter = opts.filter;
     }
     var arrayFormat;
-    if (opts.arrayFormat in arrayPrefixGenerators) {
+    if (has.call(arrayPrefixGenerators, opts.arrayFormat)) {
       arrayFormat = opts.arrayFormat;
     } else if ("indices" in opts) {
       arrayFormat = opts.indices ? "indices" : "repeat";
@@ -24753,7 +24872,7 @@ var require_stringify = __commonJS((exports, module) => {
       filter = options.filter;
       obj = filter("", obj);
     } else if (isArray(options.filter)) {
-      filter = options.filter;
+      filter = options.filter.slice();
       objKeys = filter;
     }
     var keys = [];
@@ -24779,7 +24898,7 @@ var require_stringify = __commonJS((exports, module) => {
         continue;
       }
       var encodedKey = options.encodeDotInKeys ? String(key).replace(/\./g, "%2E") : String(key);
-      pushToArray(keys, stringify(value, encodedKey, generateArrayPrefix, commaRoundTrip, options.allowEmptyArrays, options.strictNullHandling, options.skipNulls, options.encodeDotInKeys, options.encode ? options.encoder : null, options.filter, options.sort, options.allowDots, options.serializeDate, options.format, options.formatter, options.encodeValuesOnly, options.charset, sideChannel, options.depth, 0));
+      pushToArray(keys, stringify(value, encodedKey, generateArrayPrefix, commaRoundTrip, options.allowEmptyArrays, options.strictNullHandling, options.skipNulls, options.encodeDotInKeys, options.encode ? options.encoder : null, filter, options.sort, options.allowDots, options.serializeDate, options.format, options.formatter, options.encodeValuesOnly, options.charset, sideChannel, options.depth, 0));
     }
     var joined = keys.join(options.delimiter);
     var prefix = options.addQueryPrefix === true ? "?" : "";
@@ -24794,11 +24913,56 @@ var require_stringify = __commonJS((exports, module) => {
   };
 });
 
-// ../../node_modules/.bun/qs@6.16.0/node_modules/qs/lib/parse.js
+// ../../node_modules/.bun/qs@6.17.1/node_modules/qs/lib/parse.js
 var require_parse = __commonJS((exports, module) => {
+  var getSideChannel = require_side_channel();
   var utils = require_utils();
   var has = Object.prototype.hasOwnProperty;
   var isArray = Array.isArray;
+  var getPrototypeOf = Object.getPrototypeOf;
+  var fromCharCode = String.fromCharCode;
+  var isPlainContainer = function isPlainContainer2(value) {
+    if (!value || typeof value !== "object") {
+      return false;
+    }
+    if (isArray(value)) {
+      return true;
+    }
+    var proto = getPrototypeOf(value);
+    return proto === Object.prototype || proto === null;
+  };
+  var emptyCopyOf = function emptyCopyOf2(value) {
+    if (isArray(value)) {
+      var arr = [];
+      arr.length = value.length;
+      return arr;
+    }
+    return getPrototypeOf(value) === null ? { __proto__: null } : {};
+  };
+  var copyInput = function copyInput2(input2) {
+    var copies = getSideChannel();
+    var result = {};
+    var queue = [{ source: input2, target: result }];
+    for (var i2 = 0;i2 < queue.length; ++i2) {
+      var source = queue[i2].source;
+      var target = queue[i2].target;
+      var keys = Object.keys(source);
+      for (var j2 = 0;j2 < keys.length; ++j2) {
+        var value = source[keys[j2]];
+        if (isPlainContainer(value)) {
+          if (!copies.has(value)) {
+            var copy = emptyCopyOf(value);
+            copies.set(value, copy);
+            queue[queue.length] = { source: value, target: copy };
+          }
+          utils.setProperty(target, keys[j2], copies.get(value));
+        } else {
+          utils.setProperty(target, keys[j2], value);
+        }
+      }
+    }
+    return result;
+  };
   var defaults = {
     allowDots: false,
     allowEmptyArrays: false,
@@ -24825,7 +24989,12 @@ var require_parse = __commonJS((exports, module) => {
   };
   var interpretNumericEntities = function(str) {
     return str.replace(/&#(\d+);/g, function($0, numberStr) {
-      return String.fromCharCode(parseInt(numberStr, 10));
+      var c2 = parseInt(numberStr, 10);
+      if (c2 > 65535 && c2 <= 1114111) {
+        c2 -= 65536;
+        return fromCharCode(55296 | c2 >> 10, 56320 | c2 & 1023);
+      }
+      return fromCharCode(c2);
     });
   };
   var parseArrayValue = function(val, options, currentArrayLength) {
@@ -24843,7 +25012,7 @@ var require_parse = __commonJS((exports, module) => {
       }
       return val.split(",");
     }
-    if (options.throwOnLimitExceeded && currentArrayLength >= options.arrayLimit) {
+    if (options.throwOnLimitExceeded && currentArrayLength >= options.arrayLimit && currentArrayLength > 0) {
       throw new RangeError("Array limit exceeded. Only " + options.arrayLimit + " element" + (options.arrayLimit === 1 ? "" : "s") + " allowed in an array.");
     }
     return val;
@@ -24882,6 +25051,7 @@ var require_parse = __commonJS((exports, module) => {
       var part = parts[i2];
       var bracketEqualsPos = part.indexOf("]=");
       var pos = bracketEqualsPos === -1 ? part.indexOf("=") : bracketEqualsPos + 1;
+      var isEmptyBracketKey = pos > 1 && part.slice(pos - 2, pos) === "[]";
       var key;
       var val;
       if (pos === -1) {
@@ -24890,15 +25060,17 @@ var require_parse = __commonJS((exports, module) => {
       } else {
         key = options.decoder(part.slice(0, pos), defaults.decoder, charset, "key");
         if (key !== null) {
-          val = utils.maybeMap(parseArrayValue(part.slice(pos + 1), options, isArray(obj[key]) ? obj[key].length : 0), function(encodedVal) {
+          val = utils.maybeMap(parseArrayValue(part.slice(pos + 1), options, isArray(obj[key]) && (options.duplicates === "combine" || isEmptyBracketKey) ? obj[key].length : 0), function(encodedVal) {
             return options.decoder(encodedVal, defaults.decoder, charset, "value");
           });
         }
       }
       if (val && options.interpretNumericEntities && charset === "iso-8859-1") {
-        val = interpretNumericEntities(String(val));
+        val = utils.maybeMap(val, function(value) {
+          return value ? interpretNumericEntities(String(value)) : value;
+        });
       }
-      if (part.indexOf("[]=") > -1) {
+      if (isEmptyBracketKey) {
         val = isArray(val) ? [val] : val;
       }
       if (options.comma && isArray(val) && val.length > options.arrayLimit) {
@@ -24906,7 +25078,7 @@ var require_parse = __commonJS((exports, module) => {
       }
       if (key !== null) {
         var existing = has.call(obj, key);
-        if (existing && (options.duplicates === "combine" || part.indexOf("[]=") > -1)) {
+        if (existing && (options.duplicates === "combine" || isEmptyBracketKey)) {
           obj[key] = utils.combine(obj[key], val, options.arrayLimit, options.plainObjects, options.throwOnLimitExceeded);
         } else if (!existing || options.duplicates === "last") {
           obj[key] = val;
@@ -24915,6 +25087,9 @@ var require_parse = __commonJS((exports, module) => {
     }
     return obj;
   };
+  var stripWrappingBrackets = function stripWrappingBrackets2(key) {
+    return key.charAt(0) === "[" && key.charAt(key.length - 1) === "]" ? key.slice(1, -1) : key;
+  };
   var parseObject = function(chain, val, options, valuesParsed) {
     var currentArrayLength = 0;
     if (chain.length > 0 && chain[chain.length - 1] === "[]") {
@@ -24933,12 +25108,12 @@ var require_parse = __commonJS((exports, module) => {
         }
       } else {
         obj = options.plainObjects ? { __proto__: null } : {};
-        var cleanRoot = root.charAt(0) === "[" && root.charAt(root.length - 1) === "]" ? root.slice(1, -1) : root;
-        var decodedRoot = options.decodeDotInKeys ? cleanRoot.replace(/%2E/g, ".") : cleanRoot;
+        var cleanRoot = stripWrappingBrackets(root);
+        var decodedRoot = options.decodeDotInKeys ? cleanRoot.replace(/%2E/gi, ".") : cleanRoot;
         var index = parseInt(decodedRoot, 10);
         var isValidArrayIndex = !isNaN(index) && root !== decodedRoot && String(index) === decodedRoot && index >= 0 && options.parseArrays;
         if (!options.parseArrays && decodedRoot === "") {
-          obj = { 0: leaf };
+          obj[0] = leaf;
         } else if (isValidArrayIndex && index < options.arrayLimit) {
           obj = [];
           obj[index] = leaf;
@@ -24955,10 +25130,37 @@ var require_parse = __commonJS((exports, module) => {
     }
     return leaf;
   };
+  var topLevelDotsToBrackets = function topLevelDotsToBrackets2(key) {
+    var result = "";
+    var depth = 0;
+    for (var i2 = 0;i2 < key.length; i2 += 1) {
+      var cu = key.charCodeAt(i2);
+      if (cu === 91) {
+        depth += 1;
+        result += "[";
+      } else if (cu === 93) {
+        if (depth > 0) {
+          depth -= 1;
+        }
+        result += "]";
+      } else if (cu === 46 && depth === 0 && i2 + 1 < key.length && key.charCodeAt(i2 + 1) !== 46 && key.charCodeAt(i2 + 1) !== 91) {
+        var start = i2 + 1;
+        var j2 = start;
+        while (j2 < key.length && key.charCodeAt(j2) !== 46 && key.charCodeAt(j2) !== 91) {
+          j2 += 1;
+        }
+        result += "[" + key.slice(start, j2) + "]";
+        i2 = j2 - 1;
+      } else {
+        result += key.charAt(i2);
+      }
+    }
+    return result;
+  };
   var splitKeyIntoSegments = function splitKeyIntoSegments2(originalKey, options) {
-    var key = options.allowDots ? originalKey.replace(/\.([^.[]+)/g, "[$1]") : originalKey;
+    var key = options.allowDots ? topLevelDotsToBrackets(originalKey) : originalKey;
     if (options.depth <= 0) {
-      if (!options.plainObjects && has.call(Object.prototype, key)) {
+      if (!options.plainObjects && has.call(Object.prototype, stripWrappingBrackets(key))) {
         if (!options.allowPrototypes) {
           return;
         }
@@ -25081,7 +25283,7 @@ var require_parse = __commonJS((exports, module) => {
     if (str === "" || str === null || typeof str === "undefined") {
       return options.plainObjects ? { __proto__: null } : {};
     }
-    var tempObj = typeof str === "string" ? parseValues(str, options) : str;
+    var tempObj = typeof str === "string" ? parseValues(str, options) : copyInput(str);
     var obj = options.plainObjects ? { __proto__: null } : {};
     var keys = Object.keys(tempObj);
     for (var i2 = 0;i2 < keys.length; ++i2) {
@@ -25096,7 +25298,7 @@ var require_parse = __commonJS((exports, module) => {
   };
 });
 
-// ../../node_modules/.bun/qs@6.16.0/node_modules/qs/lib/index.js
+// ../../node_modules/.bun/qs@6.17.1/node_modules/qs/lib/index.js
 var require_lib = __commonJS((exports, module) => {
   var stringify = require_stringify();
   var parse5 = require_parse();
@@ -99784,7 +99986,7 @@ var program = new Command;
 
 // package.json
 var name = "@sppg2001/atomize";
-var version2 = "5.1.1";
+var version2 = "5.1.3";
 
 // src/cli/commands/auth/auth-add.command.ts
 init_dist6();
@@ -105180,7 +105382,9 @@ function applyProposalToYaml(sourceYaml, proposal) {
   const doc2 = $parseDocument(sourceYaml);
   if (deepEqual2(doc2.toJS(), proposal))
     return sourceYaml;
-  doc2.contents = merge2(doc2, doc2.contents, proposal);
+  const aliases = new Map;
+  doc2.contents = merge2(doc2, doc2.contents, proposal, aliases);
+  expandStaleAliases(doc2, aliases);
   return doc2.toString(detectIndentation(sourceYaml));
 }
 function deriveImprovedCopy(proposal, source) {
@@ -105191,7 +105395,11 @@ function deriveImprovedCopy(proposal, source) {
     ...source.catalogRef ? { origin: source.catalogRef } : {}
   };
 }
-function merge2(doc2, node2, value) {
+function merge2(doc2, node2, value, aliases) {
+  if ($isAlias(node2)) {
+    aliases.set(node2, value);
+    return node2;
+  }
   if (isPlainObject4(value) && $isMap(node2)) {
     for (const pair of [...node2.items]) {
       const key = $isScalar(pair.key) ? pair.key.value : pair.key;
@@ -105202,7 +105410,7 @@ function merge2(doc2, node2, value) {
       if (child === undefined)
         continue;
       const existing = node2.get(key, true);
-      node2.set(key, existing === undefined ? doc2.createNode(child) : merge2(doc2, existing, child));
+      node2.set(key, existing === undefined ? doc2.createNode(child) : merge2(doc2, existing, child, aliases));
     }
     return node2;
   }
@@ -105218,7 +105426,7 @@ function merge2(doc2, node2, value) {
       if (index < 0)
         return doc2.createNode(item);
       const [match] = unused.splice(index, 1);
-      return merge2(doc2, match, item);
+      return merge2(doc2, match, item, aliases);
     });
     return node2;
   }
@@ -105229,6 +105437,25 @@ function merge2(doc2, node2, value) {
   }
   return doc2.createNode(value);
 }
+function expandStaleAliases(doc2, aliases) {
+  if (aliases.size === 0)
+    return;
+  const anchors = new Map;
+  $visit(doc2, {
+    Node(_key, node2) {
+      if (!$isAlias(node2)) {
+        if (node2.anchor)
+          anchors.set(node2.anchor, node2);
+        return;
+      }
+      if (!aliases.has(node2))
+        return;
+      const value = aliases.get(node2);
+      const target = anchors.get(node2.source);
+      return target && deepEqual2(target.toJS(doc2), value) ? undefined : doc2.createNode(value);
+    }
+  });
+}
 function sameItem(node2, value) {
   if ($isScalar(node2))
     return node2.value === value;

package/package.json

@@ -1,6 +1,6 @@
 {
 	"name": "@sppg2001/atomize",
-	"version": "5.1.1",
+	"version": "5.1.3",
 	"description": "Automatically generate tasks from user stories with smart templates",
 	"type": "module",
 	"main": "./dist/cli/index.js",