feat: update Makefile and README for new linting and testing commands; refactor credential storage to JSON format

uv.lock

@@ -170,7 +170,6 @@ source = { editable = "." }
 dependencies = [
     { name = "plankapy", version = "2.2.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.13'" },
     { name = "plankapy", version = "2.3.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.13'" },
-    { name = "python-dotenv" },
     { name = "rich" },
     { name = "typer" },
 ]
@@ -185,7 +184,6 @@ dev = [
 [package.metadata]
 requires-dist = [
     { name = "plankapy", specifier = ">=2.2.2" },
-    { name = "python-dotenv" },
     { name = "rich" },
     { name = "typer" },
 ]
@@ -299,15 +297,6 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/3b/ab/b3226f0bd7cdcf710fbede2b3548584366da3b19b5021e74f5bde2a8fa3f/pytest-9.0.2-py3-none-any.whl", hash = "sha256:711ffd45bf766d5264d487b917733b453d917afd2b0ad65223959f59089f875b", size = 374801, upload-time = "2025-12-06T21:30:49.154Z" },
 ]
 
-[[package]]
-name = "python-dotenv"
-version = "1.2.1"
-source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/f0/26/19cadc79a718c5edbec86fd4919a6b6d3f681039a2f6d66d14be94e75fb9/python_dotenv-1.2.1.tar.gz", hash = "sha256:42667e897e16ab0d66954af0e60a9caa94f0fd4ecf3aaf6d2d260eec1aa36ad6", size = 44221, upload-time = "2025-10-26T15:12:10.434Z" }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/14/1b/a298b06749107c305e1fe0f814c6c74aea7b2f1e10989cb30f544a1b3253/python_dotenv-1.2.1-py3-none-any.whl", hash = "sha256:b81ee9561e9ca4004139c6cbba3a238c32b03e4894671e181b671e8cb8425d61", size = 21230, upload-time = "2025-10-26T15:12:09.109Z" },
-]
-
 [[package]]
 name = "pywin32-ctypes"
 version = "0.2.3"