Release 0.4.1: plugin.json holds the only version

.claude-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "cell-type-annotation",
-  "version": "0.4.0",
+  "version": "0.4.1",
   "description": "Evidence-driven cell-type annotation of pre-clustered single-cell and spatial transcriptomics data: Claude annotates level by level, one routed cross-check per level, signed-off assumptions, critic subagents. Ships a skill and the cell_type_annotation Python package; runs as an analysis-workflow task.",
   "author": {
     "name": "quadbio"

README.md

@@ -38,11 +38,12 @@ It requires the [knowledgebase MCP](https://github.com/biocontext-ai/knowledgeba
 
 The plugin, once per machine, from the [quadbio marketplace](https://github.com/quadbio/claude-plugins).
 
-The package, in the analysis repo's `pixi.toml`, next to the scverse stack the task scripts use:
+The package, in the analysis repo's `pixi.toml` (its lock pins the commit), next to the scverse stack the task
+scripts use:
 
 ```toml
 [pypi-dependencies]
-cell-type-annotation = { git = "https://github.com/quadbio/cell-type-annotation", tag = "v0.4.0" }
+cell-type-annotation = { git = "https://github.com/quadbio/cell-type-annotation" }
 ```
 
 Cross-check tools (celltypist, cellmapper, panhumanpy, scvi-tools, scimilarity) are added as a run needs them. Their
@@ -73,9 +74,8 @@ For live package edits in an analysis repo, depend on the checkout:
 
 ## Release
 
-1. Bump `version` in both `pyproject.toml` and `.claude-plugin/plugin.json` (a test checks they agree).
-2. Tag `vX.Y.Z`.
-3. Bump the `ref` in [quadbio/claude-plugins](https://github.com/quadbio/claude-plugins).
+Bump `version` in `.claude-plugin/plugin.json` and merge: the marketplace follows `main`, and users update when the
+version changes.
 
 ## License
 

pyproject.toml

@@ -4,7 +4,6 @@ requires = [ "hatchling" ]
 
 [project]
 name = "cell-type-annotation"
-version = "0.4.0"
 description = "Method routing, evidence checks, label hierarchies and reports for evidence-driven cell-type annotation."
 readme = "README.md"
 license = "MIT"
@@ -16,13 +15,16 @@ classifiers = [
   "Programming Language :: Python :: 3.13",
   "Programming Language :: Python :: 3.14",
 ]
+dynamic = [ "version" ]
 dependencies = [ "anndata>=0.12", "matplotlib>=3.8", "numpy>=2", "pandas>=2", "scipy" ]
 urls.Source = "https://github.com/quadbio/cell-type-annotation"
 
 [dependency-groups]
 dev = [ "pre-commit", "pytest" ]
 
 [tool.hatch]
+version.path = ".claude-plugin/plugin.json"
+version.pattern = '"version": "(?P<version>[^"]+)"'
 build.targets.wheel.packages = [ "src/cell_type_annotation" ]
 
 [tool.ruff]