diff --git a/.claude/skills/memray/SKILL.md b/.claude/skills/memray/SKILL.md
index 79f704ea6..94f2feaed 100644
--- a/.claude/skills/memray/SKILL.md
+++ b/.claude/skills/memray/SKILL.md
@@ -1,9 +1,8 @@
 ---
-
 name: memray
 description: Profile the memory usage of a Python script using memray and visualize a temporal flamegraph in the browser. Use when the user wants to investigate memory consumption, find leaks, or understand allocation patterns.
 compatibility: Requires the pixi profiling environment (pixi run -e profiling). Supports Linux and macOS.
-allowed-tools: Bash(pixi run -e profiling memray-run:_) Bash(pixi run -e profiling memray-flame:_) Bash(open:_) Bash(xdg-open:_) Bash(python -m webbrowser:*)
+allowed-tools: Bash(pixi run -e profiling memray-run:*) Bash(pixi run -e profiling memray-flame:*) Bash(open:*) Bash(xdg-open:*) Bash(python -m webbrowser:*)
 ---
 
 ## Steps
@@ -12,24 +11,24 @@ allowed-tools: Bash(pixi run -e profiling memray-run:_) Bash(pixi run -e profili
 
 2. Run the script under memray:
 
-   ```bash
-   pixi run -e profiling memray-run script.py
-   ```
+    ```bash
+    pixi run -e profiling memray-run script.py
+    ```
 
-   This produces a binary file named `memray-script.py.<pid>.bin` in the current directory.
+    This produces a binary file named `memray-script.py.<pid>.bin` in the current directory.
 
 3. Generate the flamegraph HTML report from the `.bin` file:
 
-   ```bash
-   pixi run -e profiling memray-flame memray-script.py.<pid>.bin
-   ```
+    ```bash
+    pixi run -e profiling memray-flame memray-script.py.<pid>.bin
+    ```
 
-   Replace `<pid>` with the actual PID shown in the filename. This writes `memray-flamegraph-script.py.<pid>.html`.
+    Replace `<pid>` with the actual PID shown in the filename. This writes `memray-flamegraph-script.py.<pid>.html`.
 
 4. Open the report in the browser:
-   - macOS: `open memray-flamegraph-script.py.<pid>.html`
-     - Linux: `xdg-open memray-flamegraph-script.py.<pid>.html`
-       - Either: `python -m webbrowser memray-flamegraph-script.py.<pid>.html`
+    - macOS: `open memray-flamegraph-script.py.<pid>.html`
+    - Linux: `xdg-open memray-flamegraph-script.py.<pid>.html`
+    - Either: `python -m webbrowser memray-flamegraph-script.py.<pid>.html`
 
 ## Notes
 
diff --git a/.claude/skills/profimp/SKILL.md b/.claude/skills/profimp/SKILL.md
index 5f54fa007..2da0903a8 100644
--- a/.claude/skills/profimp/SKILL.md
+++ b/.claude/skills/profimp/SKILL.md
@@ -1,17 +1,16 @@
 ---
-
 name: profimp
 description: Profile Python import time using profimp and open a waterfall HTML report. Use when investigating slow startup or wanting to identify which imports are most expensive.
 compatibility: Requires profimp (available as a pixi dependency). macOS or Linux.
-allowed-tools: Bash(profimp:_) Bash(open:_) Bash(xdg-open:_) Bash(python -m webbrowser:_)
+allowed-tools: Bash(profimp:*) Bash(open:*) Bash(xdg-open:*) Bash(python -m webbrowser:*)
 ---
 
 ## Steps
 
 1. Ask what to profile. Suggest common patterns for this repo:
-   - `import spatialdata`
-     - `from spatialdata import SpatialData`
-       - `from spatialdata_io import xenium`
+    - `import spatialdata`
+    - `from spatialdata import SpatialData`
+    - `from spatialdata_io import xenium`
 
 2. Run:
 
@@ -20,9 +19,9 @@ profimp --html "<import_stmt>" > /tmp/profimp.html
 ```
 
 3. Open the report:
-   - macOS: `open /tmp/profimp.html`
-     - Linux: `xdg-open /tmp/profimp.html`
-       - Either: `python -m webbrowser /tmp/profimp.html`
+    - macOS: `open /tmp/profimp.html`
+    - Linux: `xdg-open /tmp/profimp.html`
+    - Either: `python -m webbrowser /tmp/profimp.html`
 
 ## Notes
 
diff --git a/.claude/skills/pyspy/SKILL.md b/.claude/skills/pyspy/SKILL.md
index 97c9a487f..00c6408c7 100644
--- a/.claude/skills/pyspy/SKILL.md
+++ b/.claude/skills/pyspy/SKILL.md
@@ -1,9 +1,8 @@
 ---
-
 name: pyspy
 description: Profile the execution time of a Python script using py-spy and visualize the result with speedscope. Use when the user wants to benchmark performance, find slow code paths, or profile CPU time.
 compatibility: Requires the pixi profiling environment (pixi run -e profiling). Speedscope must be installed separately (npm install -g speedscope). sudo is required on macOS.
-allowed-tools: Bash(pixi run -e profiling pyspy:_) Bash(pixi run -e profiling speedscope:_) Bash(sudo pixi run -e profiling pyspy:*)
+allowed-tools: Bash(pixi run -e profiling pyspy:*) Bash(pixi run -e profiling speedscope:*) Bash(sudo pixi run -e profiling pyspy:*)
 ---
 
 ## Steps
@@ -12,33 +11,31 @@ allowed-tools: Bash(pixi run -e profiling pyspy:_) Bash(pixi run -e profiling sp
 
 2. Run py-spy to record the profile. The output is always written to `profile.speedscope.json` in the current directory.
 
-   **Linux** (no sudo needed):
+    **Linux** (no sudo needed):
 
-   ```bash
-   pixi run -e profiling pyspy script.py
-   ```
+    ```bash
+    pixi run -e profiling pyspy script.py
+    ```
 
-   **macOS** (sudo required — py-spy needs to attach to the process):
+    **macOS** (sudo required — py-spy needs to attach to the process):
 
-   ```bash
-   sudo pixi run -e profiling pyspy script.py
-   ```
+    ```bash
+    sudo pixi run -e profiling pyspy script.py
+    ```
 
-   If sudo fails to find the pixi environment, use absolute paths:
+    If sudo fails to find the pixi environment, use absolute paths:
 
-   ```bash
-   sudo /path/to/.pixi/envs/profiling/bin/py-spy record --gil \
-     -o profile.speedscope.json --format speedscope \
-     -- /path/to/.pixi/envs/profiling/bin/python script.py
-   ```
+    ```bash
+    sudo /path/to/.pixi/envs/profiling/bin/py-spy record --gil \
+      -o profile.speedscope.json --format speedscope \
+      -- /path/to/.pixi/envs/profiling/bin/python script.py
+    ```
 
 3. Open the result in speedscope:
-
-   ```bash
-   pixi run -e profiling speedscope
-   ```
-
-   This opens `profile.speedscope.json` in the browser via the local speedscope CLI.
+    ```bash
+    pixi run -e profiling speedscope
+    ```
+    This opens `profile.speedscope.json` in the browser via the local speedscope CLI.
 
 ## Notes
 
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 1a6258fd8..0debe4dd8 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -12,6 +12,7 @@ repos:
           - id: biome-format
             exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
             groups: [format]
+            # further file exclusions and other options are configured in biome.jsonc
     - repo: https://github.com/tox-dev/pyproject-fmt
       rev: v2.30.3
       hooks:
diff --git a/biome.jsonc b/biome.jsonc
index a70f80c13..6fa28f0cd 100644
--- a/biome.jsonc
+++ b/biome.jsonc
@@ -1,5 +1,5 @@
 {
-    "$schema": "https://biomejs.dev/schemas/2.6.3/schema.json",
+    "$schema": "https://biomejs.dev/schemas/2.6.4/schema.json",
     "vcs": { "enabled": true, "clientKind": "git", "useIgnoreFile": true },
     "formatter": { "useEditorconfig": true },
     "overrides": [
@@ -19,4 +19,11 @@
             "json": { "parser": { "allowComments": true } },
         },
     ],
+    "files": {
+        "includes": [
+            "**",
+            // Claude Code skills and settings, not project source.
+            "!.claude",
+        ],
+    },
 }