ENH: Remove legacy shell scripts, add pre-commit hooks, drop Python 3.9

Removes unused and outdated shell scripts and legacy build utilities
superseded by the new Python build system. Adds pre-commit hooks with
linting applied across the codebase. Drops Python 3.9 support as it is
EOL. Includes README and documentation updates for the new build workflow.

Author: CavRiley

.gitattributes

@@ -0,0 +1,2 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,37 @@
+---
+name: Bug report
+about: Something is broken in the build or packaging pipeline
+title: "fix: "
+labels: bug
+assignees: ""
+---
+
+## Environment
+
+- **OS / Platform**: <!-- e.g. Ubuntu 22.04 x86_64, macOS 14 arm64, Windows Server 2022 -->
+- **Python version**: <!-- e.g. 3.11.9 -->
+- **ITK version / branch**: <!-- e.g. v5.4.0, or commit hash -->
+- **Script / entry point used**: <!-- e.g. scripts/build_wheels.py, dockcross-manylinux-build-wheels.sh -->
+
+## Steps to Reproduce
+
+
+## Expected Behavior
+
+<!-- What should happen. -->
+
+## Actual Behavior
+
+<!-- What actually happens. Paste relevant log output below. -->
+
+<details>
+<summary>Log output</summary>
+
+```
+```
+
+</details>
+
+## Additional Context
+
+<!-- build_report.json contents, Docker image tag, CMake args, etc. -->

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,8 @@
+blank_issues_enabled: true
+contact_links:
+  - name: ITK Discourse (questions & support)
+    url: https://discourse.itk.org
+    about: For build questions or general ITK support, please use the ITK Discourse forum.
+  - name: ITK Documentation
+    url: https://itkpythonpackage.readthedocs.io
+    about: Check the docs before filing an issue.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,23 @@
+---
+name: Feature request
+about: Suggest a new capability or improvement to the build/packaging pipeline
+title: "feat: "
+labels: enhancement
+assignees: ""
+---
+
+## Problem / Motivation
+
+<!-- What limitation or pain point does this address? -->
+
+## Proposed Solution
+
+<!-- Describe what you'd like to see added or changed. -->
+
+## Alternatives Considered
+
+<!-- Any other approaches you've thought about? -->
+
+## Additional Context
+
+<!-- Platform relevance, ITK module context, links, etc. -->

.github/pull_request_template.md

@@ -0,0 +1,30 @@
+## Summary
+
+<!-- One or two sentences describing what this PR does and why. -->
+
+## Type of Change
+
+- [ ] Bug fix
+- [ ] New feature / enhancement
+- [ ] Refactor / cleanup
+- [ ] Docs / CI only
+
+## Checklist
+
+- [ ] Pre-commit hooks pass locally (`pre-commit run --all-files`)
+- [ ] Tested wheel build on affected platform(s) (Linux / macOS / Windows)
+- [ ] Docs updated if behavior changed (`docs/`)
+- [ ] Commit messages follow Conventional Commits (`feat:`, `fix:`, `chore:`, etc.)
+
+## Platform(s) Tested
+
+<!-- Check all that apply, or note "untested" where applicable. -->
+- [ ] Linux x86_64 (manylinux)
+- [ ] Linux aarch64 (manylinux)
+- [ ] macOS x86_64
+- [ ] macOS arm64
+- [ ] Windows x86_64
+
+## Related Issues
+
+<!-- Closes #... -->

.github/workflows/pre-commit.yaml

@@ -0,0 +1,16 @@
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - uses: pre-commit/action@v3.0.1

.gitignore

@@ -43,7 +43,6 @@ lib
 lib64
 MANIFEST
 oneTBB-prefix/
-pyproject.toml
 
 # Installer logs
 pip-log.txt
@@ -73,3 +72,7 @@ docs/_build
 # IDE junk
 .idea/*
 *.swp
+/itkVersion.py
+# pixi environments
+.pixi/*
+!.pixi/config.toml

.pre-commit-config.yaml

@@ -1,4 +1,73 @@
+# Pre-commit configuration for ITKPythonPackage
+# Run `pre-commit install` to install git hooks locally
+# Run `pre-commit run --all-files` to check all files
+# Run `pre-commit autoupdate` to update hook versions
+
+# Exclude generated/vendored directories from all hooks
+exclude: ^(\.pixi|build|pixi.lock|docs)/
+
 repos:
+  # General file hygiene
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+        stages: [pre-commit]
+      - id: end-of-file-fixer
+        stages: [pre-commit]
+      - id: check-yaml
+        stages: [pre-commit]
+      - id: check-toml
+        stages: [pre-commit]
+      - id: check-merge-conflict
+        stages: [pre-commit]
+      - id: check-added-large-files
+        args: [--maxkb=500]
+        stages: [pre-commit]
+      # Enforce LF line endings everywhere except Windows PowerShell scripts
+      - id: mixed-line-ending
+        args: [--fix=lf]
+        exclude: \.ps1$
+        stages: [pre-commit]
+
+  # Python: formatting
+  - repo: https://github.com/psf/black
+    rev: 24.10.0
+    hooks:
+      - id: black
+        stages: [pre-commit]
+
+  # Python: linting + import sorting
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.8.6
+    hooks:
+      - id: ruff
+        args: [--fix]
+        stages: [pre-commit]
+
+  # Shell: linting
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: v0.10.0.1
+    hooks:
+      - id: shellcheck
+        stages: [pre-commit]
+
+  # Shell: formatting
+  - repo: https://github.com/scop/pre-commit-shfmt
+    rev: v3.12.0-2
+    hooks:
+      - id: shfmt
+        args: [-i, "2", -w]
+        stages: [pre-commit]
+
+  # TOML: formatting
+  - repo: https://github.com/ComPWA/taplo-pre-commit
+    rev: v0.9.3
+    hooks:
+      - id: taplo-format
+        stages: [pre-commit]
+
+  # ITK commit message hooks (matching ITK/Utilities/Hooks/)
   - repo: local
     hooks:
       - id: local-prepare-commit-msg