diff --git a/pyproject.toml b/pyproject.toml
index 783d6b2..daf4fea 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,7 +17,7 @@ namespaces = true
 # ----------------------------------------- Project Metadata -------------------------------------
 #
 [project]
-version = "0.0.0.dev345"
+version = "0.0.0.dev346"
 name = "ControlMan"
 dependencies = [
     "packaging >= 23.2, < 24",
@@ -33,7 +33,7 @@ dependencies = [
     "GitTidy == 0.0.0.dev56",
     "PkgData == 0.0.0.dev5",
     "PyShellMan == 0.0.0.dev20",
-    "PySyntax == 0.0.0.dev4",
+    "PySyntax == 0.0.0.dev5",
     "ExceptionMan == 0.0.0.dev30",
     "MDit == 0.0.0.dev30",
     "JSONSchemata == 0.0.0.dev29",
diff --git a/requirements.txt b/requirements.txt
index fb29658..651f85e 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -11,7 +11,7 @@ PySerials == 0.0.0.dev33
 GitTidy == 0.0.0.dev56
 PkgData == 0.0.0.dev5
 PyShellMan == 0.0.0.dev20
-PySyntax == 0.0.0.dev4
+PySyntax == 0.0.0.dev5
 ExceptionMan == 0.0.0.dev30
 MDit == 0.0.0.dev30
 JSONSchemata == 0.0.0.dev29
diff --git a/src/controlman/_data/schema/def/license-component.yaml b/src/controlman/_data/schema/def/license-component.yaml
index 63b7001..2a5608d 100644
--- a/src/controlman/_data/schema/def/license-component.yaml
+++ b/src/controlman/_data/schema/def/license-component.yaml
@@ -1,11 +1,19 @@
 $id: https://controlman.repodynamics.com/schema/license-component
 $schema: https://json-schema.org/draft/2020-12/schema
-title: License Details
+title: License Component
 type: object
 required: [ path ]
 properties:
+  type:
+    description: |
+      Type of the component, i.e., either `license` or `exception`.
+    type: string
+    enum: [ license, exception ]
+  custom:
+    description: |
+      Whether the component is a user-defined license or exception.
+    type: boolean
   path:
-    title: File Path
     description: |
       Path to the repository's
       [`LICENSE`](https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/adding-a-license-to-a-repository)
diff --git a/src/controlman/_data/schema/def/pkg.yaml b/src/controlman/_data/schema/def/pkg.yaml
index 029bed5..6c75b5b 100644
--- a/src/controlman/_data/schema/def/pkg.yaml
+++ b/src/controlman/_data/schema/def/pkg.yaml
@@ -554,13 +554,81 @@ properties:
           pip:
             path: ${{ ....path.root }}$/requirements.txt
   file:
-    title: Package documentation settings
+    description: |
+      Configurations for Python source files.
     type: object
     additionalProperties:
+      title: File Configurations
+      description: |
+        Configurations for a set of Python source files defined by a glob pattern.
       type: object
+      additionalProperties: false
+      required: [ glob ]
+      anyOf:
+        - required: [ docstring ]
+        - required: [ header_comments ]
       properties:
+        glob:
+          description: |
+            Glob pattern to match source files.
+            The pattern is relative to the [import package directory](#cccdef-pkg-path-import).
+          $ref: https://jsonschemata.repodynamics.com/string/oneline
         docstring:
-          type: string
+          description: |
+            Docstring configurations for the source files.
+          type: object
+          additionalProperties: false
+          required: [ mode, content ]
+          properties:
+            content:
+              description: |
+                Content of the docstring.
+              type: string
+            mode:
+              description: |
+                Mode of the docstring.
+              type: string
+              enum: [ append, prepend, replace ]
+              default: append
+            max_line_length:
+              description: |
+                Maximum line length of the docstring.
+              type: integer
+              minimum: 0
+        header_comments:
+          description: |
+              Header comments for the source files.
+          type: object
+          additionalProperties: false
+          required: [ mode, content ]
+          properties:
+            mode:
+              description: |
+                Mode of the header comments.
+              type: string
+              enum: [ append, prepend, replace ]
+              default: append
+            content:
+              description: |
+                  Content of the header comments.
+              type: string
+            max_line_length:
+              description: |
+                Maximum line length of the comments.
+              type: integer
+              minimum: 0
+            line_continuation_indent:
+              description: |
+                Indentation of line continuation.
+              type: integer
+              minimum: 0
+              default: 0
+            empty_lines:
+              description: |
+                Number of empty lines between comments.
+              type: integer
+              minimum: 0
+              default: 1
   manifest:
     title: MANIFEST.in configurations.
     description: |
diff --git a/src/controlman/_data/schema/main.yaml b/src/controlman/_data/schema/main.yaml
index 01da442..3a4e387 100644
--- a/src/controlman/_data/schema/main.yaml
+++ b/src/controlman/_data/schema/main.yaml
@@ -34,10 +34,9 @@ description: |
       maintenance, testing, and refactoring tasks.
 
 type: object
-required: [ repo, branch, control ]
+required: [ name, repo, branch, control ]
 properties:
   name:
-    title: Name
     description: |
       Name of the project.
 
@@ -74,7 +73,6 @@ properties:
       - My-Project
     $ref: https://jsonschemata.repodynamics.com/string/oneline
   title:
-    title: Title
     description: |
       A single-line description or slogan of the project.
       
@@ -94,7 +92,6 @@ properties:
       - Python Tools for Quantum Mechanics Simulations and Research
     $ref: https://jsonschemata.repodynamics.com/string/oneline
   abstract:
-    title: Abstract
     description: |
       A short description of the project.
       It can contain GitHub Flavored Markdown and HTML syntax,
@@ -129,7 +126,6 @@ properties:
         Cras eros risus, viverra ut lectus nec, lobortis rhoncus felis.
     $ref: https://jsonschemata.repodynamics.com/string/nonempty
   keywords:
-    title: Keywords
     description: |
       Keywords categorizing the project.
       
@@ -148,7 +144,6 @@ properties:
       - Scientific Computing
     $ref: https://jsonschemata.repodynamics.com/array/unique-strings
   highlights:
-    title: Highlights
     description: |
       Key features of the project.
       
@@ -189,7 +184,6 @@ properties:
           description: Description of the project feature.
           $ref: https://jsonschemata.repodynamics.com/string/nonempty
   license:
-    title: License
     description: |
       License of the project.
       You can either select one of the supported [SPDX](https://spdx.org/licenses/) licenses
@@ -230,27 +224,45 @@ properties:
     required: [ expression ]
     properties:
       expression:
-        title: SPDX License Expression
-        description: |
-          [SPDX](https://spdx.org/licenses/) identifier of the license.
-          If one of the supported IDs are selected,
-          the rest of the keys are automatically filled in.
-          Otherwise, `name`, `text`, and `notice` must be provided.
-          Supported IDs are:
-          
-          - `AGPL-3.0-or-later`: [GNU Affero General Public License v3 or later](https://choosealicense.com/licenses/agpl-3.0/)
-          - `AGPL-3.0`: [GNU Affero General Public License v3](https://choosealicense.com/licenses/agpl-3.0/)
-          - `GPL-3.0-or-later`: [GNU General Public License v3 or later](https://choosealicense.com/licenses/gpl-3.0/)
-          - `GPL-3.0`: [GNU General Public License v3](https://choosealicense.com/licenses/gpl-3.0/)
-          - `BSD-3-Clause`: [BSD 3-Clause "New" or "Revised" License](https://choosealicense.com/licenses/bsd-3-clause/)
-          - `BSD-2-Clause`: [BSD 2-Clause "Simplified" License](https://choosealicense.com/licenses/bsd-2-clause/)
-          - `MIT`: [MIT License](https://choosealicense.com/licenses/mit/)
-          - `BSL-1.0`: [Boost Software License 1.0](https://choosealicense.com/licenses/bsl-1.0/)
-          - `Apache-2.0`: [Apache License 2.0](https://choosealicense.com/licenses/apache-2.0/)
-          - `MPL-2.0`: [Mozilla Public License 2.0](https://choosealicense.com/licenses/mpl-2.0/)
-          - `Unlicense`: [The Unlicense](https://choosealicense.com/licenses/unlicense/)
         $ref: https://jsonschemata.repodynamics.com/string/nonempty
+        description: |
+          An [SPDX license expression](https://spdx.github.io/spdx-spec/v3.0.1/annexes/spdx-license-expressions/)
+          defining the license of the project.
+        description_examples: |
+          To select a single license from the [SPDX License List](https://spdx.org/licenses/),
+          simply provide its [SPDX license ID](https://spdx.dev/learn/handling-license-info/).
+          Some common SPDX license IDs are:
+          - `AGPL-3.0-or-later`: [GNU Affero General Public License v3.0 or later](https://spdx.org/licenses/AGPL-3.0-or-later.html)
+          - `GPL-3.0-or-later`: [GNU General Public License v3.0 or later](https://spdx.org/licenses/GPL-3.0-or-later.html)
+          - `LGPL-3.0-or-later`: [GNU Lesser General Public License v3.0 or later](https://spdx.org/licenses/LGPL-3.0-or-later.html)
+          - `Apache-2.0`: [Apache License 2.0](https://spdx.org/licenses/Apache-2.0.html)
+          - `BSL-1.0`: [Boost Software License 1.0](https://spdx.org/licenses/BSL-1.0.html)
+          - `MIT`: [MIT License](https://spdx.org/licenses/MIT.html)
+          - `BSD-3-Clause`: [BSD 3-Clause "New" or "Revised" License](https://spdx.org/licenses/BSD-3-Clause.html)
+          - `BSD-2-Clause`: [BSD 2-Clause "Simplified" License](https://spdx.org/licenses/BSD-2-Clause.html)
+          - `MPL-2.0`: [Mozilla Public License 2.0](https://spdx.org/licenses/MPL-2.0.html)
+          - `Unlicense`: [The Unlicense](https://spdx.org/licenses/Unlicense.html)
+          [Composite licenses](https://spdx.github.io/spdx-spec/v3.0.1/annexes/spdx-license-expressions/#composite-license-expressions)
+          can be defined using "OR", "AND", and "WITH" operators with parentheses:
+          - `OR`: Allows either of the licenses to be used.
+          - `AND`: Requires compliance with both licenses.
+          - `WITH`: Defines an [exception](https://spdx.org/licenses/exceptions-index.html) to the license.
+          - `(` and `)`: Grouping of expressions.
+          For example:
+            - `MIT OR GPL-3.0-or-later` allows either the `MIT` or `GPL-3.0-or-later` license to be used.
+            - `LGPL-2.1-only OR MIT OR BSD-3-Clause` allows either the `LGPL-2.1-only`, `MIT`, or `BSD-3-Clause` license to be used.
+            - `LGPL-2.1-only AND MIT` requires compliance with both the `LGPL-2.1-only` and `MIT` licenses.
+            - `GPL-2.0-or-later WITH Bison-exception-2.2` adds `Bison-exception-2.2` to the `GPL-2.0-or-later` license.
+            - `MIT AND (LGPL-2.1-or-later OR BSD-3-Clause)` requires compliance with the `MIT` license and either the `LGPL-2.1-or-later` or `BSD-3-Clause` license.
+          Custom licenses and exceptions can also be defined
+          using the `LicenseRef-` and `AdditionRef-` prefixes, respectively.
+          For example, to add a custom exception to the `MIT` license,
+          you can use `MIT WITH AdditionRef-My-Exception-1.0`.
+          The custom exception `AdditionRef-My-Exception-1.0`
+          must then be defined under [`$.license.component`](#ccc-license-component).
       component:
+        description: |
+          Information about each component of the license expression.
         type: object
         patternProperties:
           '^(DocumentRef-[a-zA-Z0-9-.]+:)?(AdditionRef|LicenseRef)-[a-zA-Z0-9.-]+$':
@@ -272,23 +284,6 @@ properties:
           header:
             default: { }
             $ref: https://controlman.repodynamics.com/schema/license-component-config
-      header:
-        title: Header
-        description: |
-          Custom license notice.
-        $ref: https://jsonschemata.repodynamics.com/string/nonempty
-      path:
-        type: object
-        additionalProperties: false
-        properties:
-          texts_plain:
-            type: array
-            items:
-              $ref: https://jsonschemata.repodynamics.com/path/posix/absolute-from-cwd
-          headers_plain:
-            type: array
-            items:
-              $ref: https://jsonschemata.repodynamics.com/path/posix/absolute-from-cwd
   copyright:
     title: Copyright
     description: |
@@ -3506,20 +3501,75 @@ properties:
     additionalProperties: false
     properties:
       duplicate:
+        description: |
+          Definition of duplicate locations for repository files.
+          Files defined here will be duplicated to the specified destinations
+          and dynamically kept in sync with the source.
+          
+          For each duplication, define a key-value pair where the key is an ID,
+          and the value is a mapping with keys `source` and `destinations`,
+          or `sources` and `destinations`.
+        description_examples: |
+          - Duplicate a file at `path/to/file.txt` to `path/to/backup/file.txt`:
+            ```yaml
+            backup_file:
+              source: path/to/file.txt
+              destinations:
+                - path/to/backup/file.txt
+            ```
+          - Duplicate a file at `path/to/file.txt` to both 
+            `path/to/backup1/backup_file.txt` and `path/to/backup2/backup_file.txt`:
+            ```yaml
+            backup_files:
+              source: path/to/file.txt
+              destinations:
+                - path/to/backup1/backup_file.txt
+                - path/to/backup2/backup_file.txt
+          - Duplicate multiple files at `path/to/file1.txt` and `path/to/file2.txt` to `path/to/backup_dir`:
+            ```yaml
+            backup_files:
+              sources:
+                - path/to/file1.txt
+                - path/to/file2.txt
+              destinations:
+                - path/to/backup_dir
+          - Duplicate all text files in `path/to/text_files` to `path/to/backup_dir`:
+            ```yaml
+            backup_files:
+              sources:
+                - path/to/text_files/*.txt
+              destinations:
+                - path/to/backup_dir
+            ```
         type: object
         additionalProperties:
+          title: Duplicate Files
           type: object
           additionalProperties: false
-          required: [ destination ]
+          required: [ destinations ]
           properties:
             source:
+              description: |
+                Path to a single file to be duplicated.
               $ref: https://jsonschemata.repodynamics.com/path/posix/absolute-from-cwd
             sources:
+              description: |
+                Paths or glob patterns for multiple files to be duplicated.
               type: array
+              uniqueItems: true
+              items:
+                $ref: https://jsonschemata.repodynamics.com/path/posix/absolute-from-cwd
+            destinations:
+              description: |
+                  Paths to the locations where the file(s) should be duplicated.
+                  When used with `source`, each path must be a full path to a file (including the filename).
+                  When used with `sources`, each path must be a directory path,
+                  where all source files are copied to, keeping their original filenames.
+              type: array
+              uniqueItems: true
+              minItems: 1
               items:
                 $ref: https://jsonschemata.repodynamics.com/path/posix/absolute-from-cwd
-            destination:
-              $ref: https://jsonschemata.repodynamics.com/path/posix/absolute-from-cwd
           oneOf:
             - required: [ source ]
             - required: [ sources ]
diff --git a/src/controlman/center_manager.py b/src/controlman/center_manager.py
index bd3a0bd..b1ab781 100644
--- a/src/controlman/center_manager.py
+++ b/src/controlman/center_manager.py
@@ -208,18 +208,24 @@ def apply_changes(self) -> None:
 
         for duplicate in self._data_before.get("file.duplicate", {}).values():
             if "source" in duplicate:
-                self._path_root.joinpath(duplicate["destination"]).unlink(missing_ok=True)
+                for destination in duplicate["destinations"]:
+                    self._path_root.joinpath(destination).unlink(missing_ok=True)
             else:
-                for source in duplicate["sources"]:
-                    self._path_root.joinpath(duplicate["destination"]).joinpath(_Path(source).stem).unlink(missing_ok=True)
+                for source_glob in duplicate["sources"]:
+                    for source in self._path_root.glob(source_glob):
+                        for destination in duplicate["destinations"]:
+                            self._path_root.joinpath(destination).joinpath(_Path(source).stem).unlink(missing_ok=True)
         for duplicate in self._data.get("file.duplicate", {}).values():
             if "source" in duplicate:
-                _shutil.copy2(self._path_root.joinpath(duplicate["source"]), self._path_root.joinpath(duplicate["destination"]))
+                for destination in duplicate["destinations"]:
+                    _shutil.copy2(self._path_root.joinpath(duplicate["source"]), self._path_root.joinpath(destination))
             else:
-                for source in duplicate["sources"]:
-                    destination_path = self._path_root.joinpath(duplicate["destination"]).joinpath(_Path(source).stem)
-                    destination_path.parent.mkdir(parents=True, exist_ok=True)
-                    _shutil.copy2(self._path_root.joinpath(source), destination_path)
+                for source_glob in duplicate["sources"]:
+                    for source in self._path_root.glob(source_glob):
+                        for destination in duplicate["destinations"]:
+                            destination_path = self._path_root.joinpath(destination).joinpath(_Path(source).stem)
+                            destination_path.parent.mkdir(parents=True, exist_ok=True)
+                            _shutil.copy2(self._path_root.joinpath(source), destination_path)
         return
 
     def _compare_dirs(self):
diff --git a/src/controlman/data_gen/main.py b/src/controlman/data_gen/main.py
index 6ea5e3a..dd8d76e 100644
--- a/src/controlman/data_gen/main.py
+++ b/src/controlman/data_gen/main.py
@@ -118,8 +118,6 @@ def _license(self):
                         json_path="license.expression",
                         data=self._data(),
                     )
-        path_texts = []
-        path_headers = []
         for spdx_ids, spdx_typ in ((license_ids, "license"), (exception_ids, "exception")):
             func = _spdx.license if spdx_typ == "license" else _spdx.exception
             class_ = _spdx.SPDXLicense if spdx_typ == "license" else _spdx.SPDXLicenseException
@@ -177,11 +175,6 @@ def _license(self):
                     raise_duplicates=False,
                     raise_type_mismatch=True,
                 )
-                path_texts.append(path_text)
-                if header_xml:
-                    path_headers.append(path_header)
-        self._data["license.path.texts_plain"] = path_texts
-        self._data["license.path.headers_plain"] = path_headers
         return
 
     def _discussion_categories(self):
diff --git a/src/controlman/file_gen/python.py b/src/controlman/file_gen/python.py
index 1232aa0..0eb7302 100644
--- a/src/controlman/file_gen/python.py
+++ b/src/controlman/file_gen/python.py
@@ -4,6 +4,7 @@
 from typing import Literal
 import textwrap
 from pathlib import Path as _Path
+import re as _re
 
 # Non-standard libraries
 import pyserials as _ps
@@ -130,9 +131,9 @@ def python_files(self) -> list[DynamicFile]:
         # Get all file glob matches
         path_to_globs_map = {}
         abs_path = self._path_repo / (self._path_import_before or self._path_import)
-        for file_glob, file_config in self._pkg.get("file", {}).items():
-            for filepath_match in abs_path.glob(file_glob):
-                path_to_globs_map.setdefault(filepath_match, []).append((file_glob, file_config))
+        for config_id, file_config in self._pkg.get("file", {}).items():
+            for filepath_match in abs_path.glob(file_config["glob"]):
+                path_to_globs_map.setdefault(filepath_match, []).append((config_id, file_config))
         if not (mapping or path_to_globs_map):
             return []
         # Process each file
@@ -140,17 +141,25 @@ def python_files(self) -> list[DynamicFile]:
         for filepath in abs_path.glob("**/*.py"):
             file_content = filepath.read_text()
             if mapping:
-                file_content = _pysyntax.modify.rename_imports(module_content=file_content, mapping=mapping)
+                file_content = _pysyntax.modify.imports(module_content=file_content, mapping=mapping)
             if filepath in path_to_globs_map:
-                for matched_glob, file_config in path_to_globs_map[filepath]:
+                for config_id, file_config in path_to_globs_map[filepath]:
                     if "docstring" in file_config:
-                        docstring_before = self._pkg_before.get("file", {}).get(matched_glob, {}).get("docstring")
+                        docstring_before = self._pkg_before.get("file", {}).get(config_id, {}).get("docstring")
                         if docstring_before != file_config["docstring"]:
                             file_content = self._update_docstring(
                                 file_content,
                                 file_config["docstring"],
                                 docstring_before,
                             )
+                    if "header_comments" in file_config:
+                        header_commens_before = self._pkg_before.get("file", {}).get(config_id, {}).get("header_comments")
+                        if header_commens_before != file_config["header_comments"]:
+                            file_content = self._update_header_comments(
+                                file_content,
+                                file_config["header_comments"],
+                                header_commens_before,
+                            )
             subtype = filepath.relative_to(self._path_repo / self._path_src)
             subtype_display = str(subtype.with_suffix("")).replace("/", ".")
             fullpath_import_before = self._path_repo / (self._path_import_before or self._path_import)
@@ -165,26 +174,85 @@ def python_files(self) -> list[DynamicFile]:
             )
         return out
 
-    def _update_docstring(self, file_content: str, template: str, template_before: str) -> str:
+    def _update_docstring(self, file_content: str, template: dict, template_before: dict) -> str:
 
-        def get_wrapped_docstring(string):
+        def get_wrapped_docstring(templ: dict) -> str:
+            max_line_length = templ.get("max_line_length")
+            if not max_line_length:
+                return templ["content"]
             lines = []
-            for line in string.strip().splitlines():
-                line_parts = textwrap.wrap(line, width=80)
+            for line in templ["content"].splitlines():
+                line_parts = textwrap.wrap(line, width=max_line_length, subsequent_indent=self._get_whitespace(line, leading=True))
                 lines.append('') if not line_parts else lines.extend(line_parts)
-            return "\n".join(lines), lines
+            wrapped_docstring = "\n".join(lines)
+            return f"{wrapped_docstring}{self._get_whitespace(templ['content'], leading=False)}"
 
-        docstring_text, docstring_lines = get_wrapped_docstring(template)
+        docstring_text = get_wrapped_docstring(template)
         docstring_before = _pysyntax.parse.docstring(file_content)
-        if docstring_before is None:
-            ending = '\n' if len(docstring_lines) > 1 else ''
-            docstring_replacement = f'{docstring_text}{ending}'
+        if template["mode"] == "replace" or docstring_before is None:
+            docstring_replacement = docstring_text
+        elif not template_before:
+            if template["mode"] == "prepend":
+                docstring_replacement = f"{docstring_text}{docstring_before}"
+            else:
+                docstring_replacement = f"{docstring_before}{docstring_text}"
+        else:
+            template_before_wrapped = get_wrapped_docstring(template_before)
+            docstring_replacement = docstring_before.replace(template_before_wrapped, "", 1)
+            if template["mode"] == "prepend":
+                docstring_replacement = f"{docstring_text}{docstring_replacement}"
+            else:
+                docstring_replacement = f"{docstring_replacement}{docstring_text}"
+        return _pysyntax.modify.docstring(file_content, docstring_replacement)
+
+
+    def _update_header_comments(self, file_content: str, template: dict, template_before: dict) -> str:
+
+        def get_wrapped_header_comments(templ: dict) -> str:
+            max_line_length = templ.get("max_line_length")
+            lines = []
+            current_newlines = 0
+            for line in templ["content"].splitlines():
+                if not line:
+                    current_newlines += 1
+                    continue
+                if current_newlines:
+                    if current_newlines == 2:
+                        lines.append('#')
+                    elif current_newlines > 2:
+                        lines.append('')
+                    current_newlines = 0
+                if max_line_length:
+                    line_indent = self._get_whitespace(line, leading=True)
+                    line_parts = textwrap.wrap(
+                        line,
+                        width=max_line_length,
+                        initial_indent=f"# {line_indent}",
+                        subsequent_indent=f"# {line_indent}{templ['line_continuation_indent'] * " "}",
+                    )
+                else:
+                    line_parts = [f"# {line}"]
+                lines.extend(line_parts)
+            return "\n".join(lines)
+
+        header_comments_text = get_wrapped_header_comments(template)
+        header_comments_before = "\n".join(_pysyntax.parse.header_comments(file_content))
+        newlines = "\n" * (template["empty_lines"] + 1)
+        if template["mode"] == "replace" or header_comments_before is None:
+            header_comments_replacement = header_comments_text
         elif not template_before:
-            docstring_replacement = f"{docstring_before.strip()}\n\n{docstring_text}\n"
+            if template["mode"] == "prepend":
+                header_comments_replacement = f"{header_comments_text}{newlines}{header_comments_before.strip()}"
+            else:
+                header_comments_replacement = f"{header_comments_before.strip()}{newlines}{header_comments_text}"
         else:
-            template_before_wrapped, _ = get_wrapped_docstring(template_before)
-            docstring_replacement = docstring_before.replace(template_before_wrapped, docstring_text, 1)
-        return _pysyntax.modify.update_docstring(file_content, docstring_replacement)
+            template_before_wrapped = get_wrapped_header_comments(template_before)
+            header_comments_replacement = header_comments_before.replace(template_before_wrapped, "", 1)
+            if template["mode"] == "prepend":
+                header_comments_replacement = f"{header_comments_text}{newlines}{header_comments_replacement.strip()}"
+            else:
+                header_comments_replacement = f"{header_comments_replacement.strip()}{newlines}{header_comments_text}"
+        return _pysyntax.modify.header_comments(file_content, header_comments_replacement)
 
     def manifest(self) -> list[DynamicFile]:
         if self.is_disabled("manifest"):
@@ -304,3 +372,8 @@ def _scripts(self, typ: Literal["cli", "gui"]) -> dict[str, str]:
         for entry in self._data.get(f"{self._type}.entry.{typ}", {}).values():
             scripts[entry["name"]] = entry["ref"]
         return scripts
+
+    @staticmethod
+    def _get_whitespace(string: str, leading: bool) -> str:
+        match = _re.match(r"^\s*", string) if leading else _re.search(r"\s*$", string)
+        return match.group() if match else ""