diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
index 1b66ddc..6fe23c7 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.md
+++ b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -8,13 +8,13 @@ assignees: ''
 ---
 
 **Describe the bug**
-A clear and concise description of what the bug is.
+A clear and concise description of the bug.
 
-**To Reproduce**
+**Steps to reproduce**
 Steps to reproduce the behavior:
 1. Go to '...'
-2. Click on '....'
-3. Scroll down to '....'
+2. Run '...'
+3. Provide '...'
 4. See error
 
 **Expected behavior**
@@ -23,9 +23,9 @@ A clear and concise description of what you expected to happen.
 **Screenshots**
 If applicable, add screenshots to help explain your problem.
 
-**Desktop (please complete the following information):**
+**Environment (please complete the following information):**
  - OS: [e.g. Linux Fedora 43, Windows 11...]
- - Version [e.g. v0.1.1]
+ - Version: [e.g. v0.1.1]
 
 **Additional context**
 Add any other context about the problem here.
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
new file mode 100644
index 0000000..b68f870
--- /dev/null
+++ b/.github/ISSUE_TEMPLATE/config.yml
@@ -0,0 +1,11 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Modelblocks project website
+    url: https://www.modelblocks.org/
+    about: Consult our website for general information on our initiative.
+  - name: Documentation
+    url: https://modelblocks.readthedocs.io/
+    about: Read our documentation for general questions and guidelines.
+  - name: Community chat
+    url: https://calliope-modelblocks.zulipchat.com
+    about: Reach out to our community on our official Zulip chat.
diff --git a/.github/workflows/template-check-version.yml b/.github/workflows/template-check-version.yml
index f99b70b..273b06a 100644
--- a/.github/workflows/template-check-version.yml
+++ b/.github/workflows/template-check-version.yml
@@ -1,54 +1,76 @@
-# Adapted from https://github.com/arup-group/actions-city-modelling-lab/blob/main/.github/workflows/template-check.yml
-# MIT licensed
+name: Deprecated reusable workflow for checking template updates
 
-name: Reusable workflow for keeping up-to-date with template changes.
 on:
   workflow_call:
 
 defaults:
   run:
-    shell: bash -l {0}
+    shell: bash --noprofile --norc -euo pipefail {0}
 
 jobs:
-  copier-issue:
+  copier-check-update:
     runs-on: ubuntu-latest
     permissions:
       contents: read
       issues: write
     env:
-      UPDATE: false
+      ISSUE_TITLE: Template update workflow migration required
     steps:
       - uses: actions/checkout@v4
 
+      - name: Warn about deprecated reusable workflow
+        run: |
+          echo "::warning title=Deprecated template check workflow::This reusable workflow and the data-module-template 'latest' tag update mechanism are deprecated. This compatibility workflow will be removed in the next template release. Update this project from the template to use the generated self-contained check-version workflow."
+
       - name: Install uv
         uses: astral-sh/setup-uv@v5
 
-      - name: Add dummy GitHub credentials
+      - name: Check for template updates
+        id: copier_check_update
         run: |
-          git config --global user.name Copier update
-          git config --global user.email check@dummy.bot.com
+          update_json="$(uvx --from 'copier>=9.15.2' copier check-update --output-format json)"
+          echo "$update_json"
+          {
+            echo "update_available=$(jq -r '.update_available // false' <<< "$update_json")"
+            echo "current_version=$(jq -r '.current_version // "unknown"' <<< "$update_json")"
+            echo "latest_version=$(jq -r '.latest_version // "unknown"' <<< "$update_json")"
+          } >> "$GITHUB_OUTPUT"
 
-      - name: Run copier update
-        run: uvx copier update --skip-answered --defaults
+      - name: Check for existing migration issue
+        id: existing_issue
+        run: |
+          issue_count="$(gh issue list \
+            --repo "${{ github.repository }}" \
+            --state open \
+            --search "$ISSUE_TITLE in:title" \
+            --json title \
+            --jq "map(select(.title == \"$ISSUE_TITLE\")) | length")"
+          if [[ "$issue_count" -gt 0 ]]; then
+            echo "exists=true" >> "$GITHUB_OUTPUT"
+          else
+            echo "exists=false" >> "$GITHUB_OUTPUT"
+          fi
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
-      - name: Wait a bit for copier cleanups
-        run: sleep 10s
+      - name: Open migration issue
+        if: steps.existing_issue.outputs.exists != 'true'
+        run: |
+          gh issue create \
+            --repo "${{ github.repository }}" \
+            --title "$ISSUE_TITLE" \
+            --body "This project is still using the deprecated reusable Modelblocks template update workflow through the data-module-template \`latest\` tag.
 
-      - name: Display differences
-        run: git status --porcelain
+          Template update available: ${{ steps.copier_check_update.outputs.update_available }}
+          Current template version: ${{ steps.copier_check_update.outputs.current_version }}
+          Latest template version: ${{ steps.copier_check_update.outputs.latest_version }}
 
-      - name: Set update flag if changes occurred
-        run: test -z "$(git status --porcelain)" || echo "UPDATE=true" >> $GITHUB_ENV
+          Please update this project from the template:
 
-      - name: Show environment variables
-        run: |
-          echo "$UPDATE"
+          \`\`\`shell
+          copier update --skip-answered --defaults
+          \`\`\`
 
-      - name: Open issue
-        if: env.UPDATE == true
-        run: |
-          gh issue --repo ${{ github.repository }} \
-          create --title "Template update" \
-          --body "A new version of the template has been published. Please update this project using \`copier update --skip-answered --defaults\` and review changes. If you need help, refer to the Modelblocks documentation or reach out to the project team."
+          The update will migrate this repository to a self-contained \`.github/workflows/check-version.yml\` workflow. This compatibility workflow will be removed in the next template release."
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/template-release.yml b/.github/workflows/template-release.yml
index 07fb57b..faae424 100644
--- a/.github/workflows/template-release.yml
+++ b/.github/workflows/template-release.yml
@@ -3,15 +3,14 @@ name: Reusable release workflow for modules
 on:
   workflow_call:
 
+defaults:
+  run:
+    shell: bash --noprofile --norc -euo pipefail {0}
+
 jobs:
-  add-latest-tag:
+  latest-tag-deprecation-warning:
     runs-on: ubuntu-latest
-    permissions:
-      contents: write
     steps:
-      - uses: actions/checkout@v4
-      - name: Run latest-tag
-        uses: EndBug/latest-tag@v1.6.2
-        with:
-          # Name of the tag.
-          ref: latest
+      - name: Warn about removed latest tag management
+        run: |
+          echo "::warning title=Deprecated template release workflow::The Modelblocks data module template no longer manages a 'latest' tag for generated projects. This compatibility workflow will be removed in the next template release. Update this project from the template to remove the generated release workflow."
diff --git a/CITATION.cff b/CITATION.cff
index 8d13e52..ba7f05f 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -10,3 +10,6 @@ authors:
   - given-names: Ivan
     family-names: Ruiz Manuel
     orcid: https://orcid.org/0000-0003-2288-6423
+  - given-names: Stefan
+    family-names: Pfenninger-Lee
+    orcid: https://orcid.org/0000-0002-8420-9498
diff --git a/copier.yaml b/copier.yaml
index 443dccb..d404f8f 100644
--- a/copier.yaml
+++ b/copier.yaml
@@ -1,9 +1,9 @@
 # === copier settings ===
-_min_copier_version: '9.4.1'
+_min_copier_version: '9.15.2'
 _subdirectory: template
 _exclude:
     # copier defaults
-    - "copier.yaml"
+    - "copier.yml"
     - "copier.yaml"
     - "~*"
     - "*.py[co]"
@@ -11,13 +11,17 @@ _exclude:
     - ".git"
     - ".DS_Store"
     - ".svn"
-    # Do not add the dummy example when updating
-    - "{% if _copier_operation == 'update' -%}workflow/envs/shell.yaml{% endif %}"
-    - "{% if _copier_operation == 'update' -%}workflow/internal/config.schema.yaml{% endif %}"
-    - "{% if _copier_operation == 'update' -%}workflow/internal/settings.yaml{% endif %}"
-    - "{% if _copier_operation == 'update' -%}workflow/rules/automatic.smk{% endif %}"
-    - "{% if _copier_operation == 'update' -%}workflow/rules/dummy.smk{% endif %}"
-    - "{% if _copier_operation == 'update' -%}workflow/scripts/dummy_script.py{% endif %}"
+    # Respect user-owned files and folders during updates.
+    - "{% if _copier_operation == 'update' -%}workflow{% endif %}"
+    - "{% if _copier_operation == 'update' -%}resources{% endif %}"
+    - "{% if _copier_operation == 'update' -%}figures{% endif %}"
+    - "{% if _copier_operation == 'update' -%}results{% endif %}"
+    - "{% if _copier_operation == 'update' -%}config/**{% endif %}"
+    - "{% if _copier_operation == 'update' -%}tests/**{% endif %}"
+    # Special cases within the above that should not be excluded.
+    - "{% if _copier_operation == 'update' -%}!config/README.md{% endif %}"
+    - "{% if _copier_operation == 'update' -%}!tests/integration_test.py{% endif %}"
+    - "{% if _copier_operation == 'update' -%}!workflow/profiles/default/config.yaml{% endif %}"
 _skip_if_exists:
   # Respect user changes, except for a few standard files.
   - config/**
@@ -26,13 +30,10 @@ _skip_if_exists:
   - results/**
   - tests/**
   - workflow/**
-  - .readthedocs.yaml
-  - AUTHORS
-  - CITATION.cff
-  - INTERFACE.yaml
-  # Special cases: these files should not be user-modified, even though they are in user-modifiable directories
+  # Special cases within the above that should not be skipped.
   - "!config/README.md"
   - "!tests/integration_test.py"
+  - "!workflow/profiles/default/config.yaml"
 _templates_suffix: .jinja
 _answers_file: .copier-answers.yml
 
diff --git a/pixi.lock b/pixi.lock
index 39e348b..6bef3f6 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -47,7 +47,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/cfgv-3.5.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/copier-9.14.1-pyhcf101f3_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/copier-9.15.2-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/distlib-0.4.3-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/dunamai-1.23.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/eval-type-backport-0.2.2-pyhd8ed1ab_0.conda
@@ -90,7 +90,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/cfgv-3.5.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/copier-9.14.1-pyhcf101f3_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/copier-9.15.2-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/distlib-0.4.3-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/dunamai-1.23.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/eval-type-backport-0.2.2-pyhd8ed1ab_0.conda
@@ -161,7 +161,7 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/cfgv-3.5.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/colorama-0.4.6-pyhd8ed1ab_1.conda
-      - conda: https://conda.anaconda.org/conda-forge/noarch/copier-9.14.1-pyhcf101f3_0.conda
+      - conda: https://conda.anaconda.org/conda-forge/noarch/copier-9.15.2-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/distlib-0.4.3-pyhcf101f3_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/dunamai-1.23.0-pyhd8ed1ab_0.conda
       - conda: https://conda.anaconda.org/conda-forge/noarch/eval-type-backport-0.2.2-pyhd8ed1ab_0.conda
@@ -670,9 +670,9 @@ packages:
   license_family: BSD
   size: 27011
   timestamp: 1733218222191
-- conda: https://conda.anaconda.org/conda-forge/noarch/copier-9.14.1-pyhcf101f3_0.conda
-  sha256: 93d1b3ba43d15010c95938b491f11d53d058a8466aa11a0a7bb51ae8cf70d3e5
-  md5: b5ddb42e9d800aacf070135d14b9423b
+- conda: https://conda.anaconda.org/conda-forge/noarch/copier-9.15.2-pyhcf101f3_0.conda
+  sha256: 9846978f01b09371e058bb795c73f246d351891871b17f6e5509e9249d947895
+  md5: 7da0d461ad7410ff9fd5607da65cd8ed
   depends:
   - python >=3.10
   - colorama >=0.4.6
@@ -693,8 +693,10 @@ packages:
   - typing_extensions >=4.0.0,<5.0.0
   - python
   license: MIT
-  size: 56002
-  timestamp: 1774962797854
+  license_family: MIT
+  run_exports: {}
+  size: 58647
+  timestamp: 1781335499983
 - conda: https://conda.anaconda.org/conda-forge/noarch/distlib-0.4.3-pyhcf101f3_0.conda
   sha256: e2753997b8bd34205f42be01b8bab8037423dc30c02a1ec12de23e5b4c0b0a2e
   md5: 58638f77697c4f6726753eb8be34818b
diff --git a/pixi.toml b/pixi.toml
index fecd0e5..84b81b7 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -10,7 +10,7 @@ homepage = "https://www.modelblocks.org/"
 
 [dependencies]
 python = ">=3.12"
-copier = ">=9.5.0"
+copier = ">=9.15.2"
 mypy = ">=1.15.0"
 pytest = ">=8.3.5"
 ruff = ">=0.9.9"
diff --git a/template/.github/ISSUE_TEMPLATE/bug_report.md b/template/.github/ISSUE_TEMPLATE/bug_report.md
index 1b66ddc..6fe23c7 100644
--- a/template/.github/ISSUE_TEMPLATE/bug_report.md
+++ b/template/.github/ISSUE_TEMPLATE/bug_report.md
@@ -8,13 +8,13 @@ assignees: ''
 ---
 
 **Describe the bug**
-A clear and concise description of what the bug is.
+A clear and concise description of the bug.
 
-**To Reproduce**
+**Steps to reproduce**
 Steps to reproduce the behavior:
 1. Go to '...'
-2. Click on '....'
-3. Scroll down to '....'
+2. Run '...'
+3. Provide '...'
 4. See error
 
 **Expected behavior**
@@ -23,9 +23,9 @@ A clear and concise description of what you expected to happen.
 **Screenshots**
 If applicable, add screenshots to help explain your problem.
 
-**Desktop (please complete the following information):**
+**Environment (please complete the following information):**
  - OS: [e.g. Linux Fedora 43, Windows 11...]
- - Version [e.g. v0.1.1]
+ - Version: [e.g. v0.1.1]
 
 **Additional context**
 Add any other context about the problem here.
diff --git a/template/.github/ISSUE_TEMPLATE/config.yaml b/template/.github/ISSUE_TEMPLATE/config.yaml
deleted file mode 100644
index 28da94d..0000000
--- a/template/.github/ISSUE_TEMPLATE/config.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-blank_issues_enabled: false
-contact_links:
-  - name: General information
-    url: https://www.modelblocks.org/
-    about: Please consult our website for general information on the Modelblocks methodology.
diff --git a/template/.github/ISSUE_TEMPLATE/config.yml b/template/.github/ISSUE_TEMPLATE/config.yml
new file mode 100644
index 0000000..b68f870
--- /dev/null
+++ b/template/.github/ISSUE_TEMPLATE/config.yml
@@ -0,0 +1,11 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Modelblocks project website
+    url: https://www.modelblocks.org/
+    about: Consult our website for general information on our initiative.
+  - name: Documentation
+    url: https://modelblocks.readthedocs.io/
+    about: Read our documentation for general questions and guidelines.
+  - name: Community chat
+    url: https://calliope-modelblocks.zulipchat.com
+    about: Reach out to our community on our official Zulip chat.
diff --git a/template/.github/workflows/check-version.yml b/template/.github/workflows/check-version.yml
index 7bde778..04e53c3 100644
--- a/template/.github/workflows/check-version.yml
+++ b/template/.github/workflows/check-version.yml
@@ -1,13 +1,75 @@
-# Check for changes in the upstream template. If changes are found, an issue is created
-name: Template check.
+# Check for changes in the upstream template. If changes are found, an issue is created.
+name: Template check
+
 on:
   workflow_dispatch:
   schedule:
     - cron: '0 0 1 * *' # Runs at 00:00 UTC on the 1st day of every month
 
+defaults:
+  run:
+    shell: bash --noprofile --norc -euo pipefail {0}
+
 jobs:
-  copier-update:
+  copier-check-update:
+    runs-on: ubuntu-latest
     permissions:
       contents: read
       issues: write
-    uses: modelblocks-org/data-module-template/.github/workflows/template-check-version.yml@latest
+    env:
+      ISSUE_TITLE: Template update available
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Check for template updates
+        id: copier_check_update
+        run: |
+          update_json="$(uvx --from 'copier>=9.15.2' copier check-update --output-format json)"
+          echo "$update_json"
+          {
+            echo "update_available=$(jq -r '.update_available // false' <<< "$update_json")"
+            echo "current_version=$(jq -r '.current_version // "unknown"' <<< "$update_json")"
+            echo "latest_version=$(jq -r '.latest_version // "unknown"' <<< "$update_json")"
+          } >> "$GITHUB_OUTPUT"
+
+      - name: Check for existing update issue
+        if: steps.copier_check_update.outputs.update_available == 'true'
+        id: existing_issue
+        run: |
+          issue_count="$(gh issue list \
+            --repo "${{ github.repository }}" \
+            --state open \
+            --search "$ISSUE_TITLE in:title" \
+            --json title \
+            --jq "map(select(.title == \"$ISSUE_TITLE\")) | length")"
+          if [[ "$issue_count" -gt 0 ]]; then
+            echo "exists=true" >> "$GITHUB_OUTPUT"
+          else
+            echo "exists=false" >> "$GITHUB_OUTPUT"
+          fi
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Open update issue
+        if: steps.copier_check_update.outputs.update_available == 'true' && steps.existing_issue.outputs.exists != 'true'
+        run: |
+          gh issue create \
+            --repo "${{ github.repository }}" \
+            --title "$ISSUE_TITLE" \
+            --body "A new version of the Modelblocks data module template is available.
+
+          Current template version: ${{ steps.copier_check_update.outputs.current_version }}
+          Latest template version: ${{ steps.copier_check_update.outputs.latest_version }}
+
+          Please update this project using:
+
+          \`\`\`shell
+          copier update --skip-answered --defaults
+          \`\`\`
+
+          Review the resulting changes before merging them."
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/template/.github/workflows/release.yml b/template/.github/workflows/release.yml
deleted file mode 100644
index 7e25226..0000000
--- a/template/.github/workflows/release.yml
+++ /dev/null
@@ -1,11 +0,0 @@
-name: Release
-
-on:
-  release:
-    types: [released]
-
-jobs:
-  release-workflow:
-    permissions:
-      contents: write
-    uses: modelblocks-org/data-module-template/.github/workflows/template-release.yml@latest
diff --git a/tests/template_test.py b/tests/template_test.py
index 3f07ca7..a710ea6 100644
--- a/tests/template_test.py
+++ b/tests/template_test.py
@@ -2,6 +2,7 @@
 
 import subprocess
 from copy import deepcopy
+from pathlib import Path
 
 import pytest
 from copier import run_copy
@@ -49,3 +50,21 @@ def test_linting(self, pixi_built):
         assert subprocess.run(
             "pixi run snakemake --lint", shell=True, check=True, cwd=pixi_built
         )
+
+    def test_github_issue_templates(self, template_path: Path, template_project: Path):
+        """The issue templating and configuration should match at both levels."""
+        issue_template_dir = Path(".github/ISSUE_TEMPLATE")
+        repo_path = template_path / issue_template_dir
+        temp_path = template_project / issue_template_dir
+
+        repo_files = sorted(path.relative_to(repo_path) for path in repo_path.iterdir())
+        temp_files = sorted(path.relative_to(temp_path) for path in temp_path.iterdir())
+        assert temp_files == repo_files
+
+        for relative_path in repo_files:
+            repo_file = repo_path / relative_path
+            generated_file = temp_path / relative_path
+
+            assert repo_file.is_file()
+            assert generated_file.is_file()
+            assert generated_file.read_text() == repo_file.read_text()