Merge mdftb_rebase into mdftb and resolve conflicts

.codecov.yml

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+fixes:
+  - "/home/runner/work/dftbplus/dftbplus::"

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve DFTB+
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+<!-- A clear and concise description of what the bug is.-->
+
+**To Reproduce**
+<!-- Steps to reproduce the behaviour:
+
+1. minimal example of how to trigger the bug (include self-contained input file)
+2. which version of DFTB+ is used (downloaded, conda-forge or build from source),
+   if built from source include the git commit, the compiler and used libraries
+3. output showing the error
+
+All input and output files required to confirm your report. -->
+
+**Expected behaviour**
+<!-- A clear and concise description of what you expected to happen, instead of what occurred -->
+
+**Additional context**
+<!-- Add any other context about the problem here.-->

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+<!-- A clear and concise description of what the problem is. -->
+
+**Describe the solution you'd like**
+<!-- A clear and concise description of what you want to happen. -->
+
+**Describe alternatives you've considered**
+<!-- A clear and concise description of any alternative solutions or features you've considered. -->
+
+**Additional context**
+<!-- Add any other context about the feature request here. -->

.github/stale.yml

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+# Configuration for probot-stale - https://github.com/probot/stale
+
+# Number of days of inactivity before an Issue or Pull Request becomes stale
+daysUntilStale: 180
+
+# Number of days of inactivity before an Issue or Pull Request with the stale label is closed.
+# Set to false to disable. If disabled, issues still need to be closed manually, but will remain marked as stale.
+daysUntilClose: 30
+
+# Only issues or pull requests with all of these labels are check if stale. Defaults to `[]` (disabled)
+onlyLabels: []
+
+# Issues or Pull Requests with these labels will never be considered stale. Set to `[]` to disable
+exemptLabels:
+  - pinned
+  - security
+  - bug
+  - enhancement
+  - "[Status] Maybe Later"
+
+# Set to true to ignore issues in a project (defaults to false)
+exemptProjects: false
+
+# Set to true to ignore issues in a milestone (defaults to false)
+exemptMilestones: false
+
+# Set to true to ignore issues with an assignee (defaults to false)
+exemptAssignees: false
+
+# Label to use when marking as stale
+staleLabel: stale
+
+# Comment to post when marking as stale. Set to `false` to disable
+#markComment: >
+#  This issue has been automatically marked as stale because it has not had
+#  recent activity. It will be closed if no further activity occurs. Thank you
+#  for your contributions.
+
+# Comment to post when removing the stale label.
+# unmarkComment: >
+#   Your comment here.
+
+# Comment to post when closing a stale Issue or Pull Request.
+# closeComment: >
+#   Your comment here.
+
+# Limit the number of actions per hour, from 1-30. Default is 30
+limitPerRun: 30
+
+# Limit to only `issues` or `pulls`
+# only: issues
+
+# Optionally, specify configuration settings that are specific to just 'issues' or 'pulls':
+pulls:
+  markComment: >
+    This pull request has been automatically marked as stale because it has not had
+    recent activity. It will be closed if no further activity occurs.
+  closeComment: >
+    This stale pull request has been automatically closed. Feel free to open a new pull request
+    if you wish your feature to be integrated into the main branch. Make sure that your changes
+    are based on the actual state of the main branch.
+
+issues:
+  markComment: >
+    This issue has been automatically marked as stale because it has not had
+    recent activity. It will be closed if no further activity occurs.
+  closeComment: >
+    This stale issue has been automatically closed.

.github/workflows.old/fortran-build.yml

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+name: CI
+on: [push, pull_request]
+
+jobs:
+  osx-build:
+    runs-on: macos-latest
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        submodules: true
+    - uses: actions/setup-python@v1
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        brew install ninja arpack gcc@8
+        pip3 install numpy
+        echo "y" | ./utils/get_opt_externals ALL
+    - name: Configure build files
+      run: FC=gfortran-8 CC=gcc-8 cmake -B_build -S. -GNinja -DCMAKE_BUILD_TYPE=Debug -DFYPP_FLAGS='-DTRAVIS' -DWITH_MPI=false -DWITH_TRANSPORT=true -DWITH_DFTD3=true -DWITH_MBD=true -DWITH_ARPACK=true -DWITH_API=true -DELSI_VERSION=0 -DLAPACK_LIBRARIES="lapack"
+    - name: Compile project from source
+      run: ninja -C _build
+    - name: Run testsuite
+      run: cd _build && OMP_NUM_THREADS=2 ctest -j 2 --output-on-failure