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diff --git a/.github/empty.txt b/.github/empty.txt
diff --git a/.github/repos.txt b/.github/repos.txt
diff --git a/docs/_issues/2018-03-26-pandas-dev-pandas-20492.md b/docs/_issues/2018-03-26-pandas-dev-pandas-20492.md
diff --git a/docs/_issues/2019-04-25-idaholab-moose-13311.md b/docs/_issues/2019-04-25-idaholab-moose-13311.md
@@ -0,0 +1,8 @@
+---
+tags: ["C-Framework","Good-first-issue","P-normal","T-task","amr","fem","finite-elements","finite-volumes","multiphysics","object-oriented","parallel","simulation"]
+title: "Better Error message from MooseUtils::tokenizeAndConvert()"
+html_url: "https://github.com/idaholab/moose/issues/13311"
+user: "friedmud"
+repo: "idaholab/moose"
+---
+
diff --git a/docs/_issues/2020-04-28-jupyterlab-jupyterlab-8298.md b/docs/_issues/2020-04-28-jupyterlab-jupyterlab-8298.md
diff --git a/docs/_issues/2021-07-12-JuliaPlots-Makie.jl-1112.md b/docs/_issues/2021-07-12-JuliaPlots-Makie.jl-1112.md
diff --git a/docs/_issues/2021-08-27-JuliaPlots-Makie.jl-1274.md b/docs/_issues/2021-08-27-JuliaPlots-Makie.jl-1274.md
diff --git a/docs/_issues/2021-12-02-sanctuuary-APE-50.md b/docs/_issues/2021-12-02-sanctuuary-APE-50.md
@@ -0,0 +1,8 @@
+---
+tags: ["automated-pipeline","java","program-synthesis","workflow-synthesis"]
+title: "Update shell script outputs to match the CWL output format"
+html_url: "https://github.com/sanctuuary/APE/issues/50"
+user: "vedran-kasalica"
+repo: "sanctuuary/APE"
+---
+
diff --git a/docs/_issues/2022-02-24-tardis-sn-carsus-274.md b/docs/_issues/2022-02-24-tardis-sn-carsus-274.md
diff --git a/docs/_issues/2022-07-15-BradyAJohnston-MolecularNodes-50.md b/docs/_issues/2022-07-15-BradyAJohnston-MolecularNodes-50.md
@@ -0,0 +1,8 @@
+---
+tags: ["biochemistry","blender","blender-addon","enhancement","geometry-nodes","help-wanted","molecular","molecular-dynamics","molecular-graphics","molecular-modeling","molecule","pdb","protein","protein-data-bank","protein-structure","protein-visualization","proteins","sciart","structural-biology","visualisation"]
+title: "Add support for Atom Indices Import"
+html_url: "https://github.com/BradyAJohnston/MolecularNodes/issues/50"
+user: "BradyAJohnston"
+repo: "BradyAJohnston/MolecularNodes"
+---
+
diff --git a/docs/_issues/2022-08-25-thomaspinder-GPJax-106.md b/docs/_issues/2022-08-25-thomaspinder-GPJax-106.md
@@ -1,5 +1,5 @@
 ---
-tags: ["bayesian-inference","documentation","enhancement","gaussian-processes","jax","machine-learning","probabilistic-programming"]
+tags: ["bayesian-inference","documentation","enhancement","gaussian-processes","jax","machine-learning","probabilistic-programming","stale"]
 title: "docs: Natgrads notebook"
 html_url: "https://github.com/JaxGaussianProcesses/GPJax/issues/106"
 user: "daniel-dodd"

diff --git a/docs/_issues/2022-08-30-TORCH-Consortium-MAGMA-120.md b/docs/_issues/2022-08-30-TORCH-Consortium-MAGMA-120.md
@@ -0,0 +1,8 @@
+---
+tags: ["enhancement","genomics","help-wanted","mycobacterium-tuberculosis","nextflow","nextflow-pipeline","pipeline","tuberculosis","wish-list"]
+title: "Thread for possible enhancements in future"
+html_url: "https://github.com/TORCH-Consortium/MAGMA/issues/120"
+user: "abhi18av"
+repo: "TORCH-Consortium/MAGMA"
+---
+
diff --git a/docs/_issues/2023-01-05-thomaspinder-GPJax-177.md b/docs/_issues/2023-01-05-thomaspinder-GPJax-177.md
@@ -1,5 +1,5 @@
 ---
-tags: ["bayesian-inference","enhancement","gaussian-processes","jax","machine-learning","probabilistic-programming"]
+tags: ["bayesian-inference","enhancement","gaussian-processes","jax","machine-learning","probabilistic-programming","stale"]
 title: "dev: Unit tests on `GaussianDistribution` object."
 html_url: "https://github.com/JaxGaussianProcesses/GPJax/issues/177"
 user: "daniel-dodd"

diff --git a/docs/_issues/2023-02-17-biopython-biopython-4238.md b/docs/_issues/2023-02-17-biopython-biopython-4238.md
diff --git a/docs/_issues/2023-05-18-thomaspinder-GPJax-268.md b/docs/_issues/2023-05-18-thomaspinder-GPJax-268.md
@@ -1,5 +1,5 @@
 ---
-tags: ["bayesian-inference","documentation","gaussian-processes","jax","machine-learning","probabilistic-programming"]
+tags: ["bayesian-inference","documentation","gaussian-processes","jax","machine-learning","probabilistic-programming","stale"]
 title: "docs: Add triangular solve figure"
 html_url: "https://github.com/JaxGaussianProcesses/GPJax/issues/268"
 user: "thomaspinder"

diff --git a/docs/_issues/2023-05-18-thomaspinder-GPJax-273.md b/docs/_issues/2023-05-18-thomaspinder-GPJax-273.md
@@ -1,5 +1,5 @@
 ---
-tags: ["bayesian-inference","enhancement","gaussian-processes","help-wanted","jax","machine-learning","probabilistic-programming"]
+tags: ["bayesian-inference","enhancement","gaussian-processes","help-wanted","jax","machine-learning","probabilistic-programming","stale"]
 title: "feat: Attach priors to parameters"
 html_url: "https://github.com/JaxGaussianProcesses/GPJax/issues/273"
 user: "thomaspinder"

diff --git a/docs/_issues/2023-05-19-Pometry-Raphtory-940.md b/docs/_issues/2023-05-19-Pometry-Raphtory-940.md
diff --git a/docs/_issues/2023-06-08-thomaspinder-GPJax-297.md b/docs/_issues/2023-06-08-thomaspinder-GPJax-297.md
@@ -1,5 +1,5 @@
 ---
-tags: ["bayesian-inference","enhancement","gaussian-processes","help-wanted","jax","machine-learning","probabilistic-programming"]
+tags: ["bayesian-inference","enhancement","gaussian-processes","help-wanted","jax","machine-learning","probabilistic-programming","stale"]
 title: "feat: Implement beta likelihood"
 html_url: "https://github.com/JaxGaussianProcesses/GPJax/issues/297"
 user: "thomaspinder"

diff --git a/docs/_issues/2023-06-08-thomaspinder-GPJax-298.md b/docs/_issues/2023-06-08-thomaspinder-GPJax-298.md
@@ -1,5 +1,5 @@
 ---
-tags: ["bayesian-inference","enhancement","gaussian-processes","help-wanted","jax","machine-learning","probabilistic-programming"]
+tags: ["bayesian-inference","enhancement","gaussian-processes","help-wanted","jax","machine-learning","probabilistic-programming","stale"]
 title: "feat: Implement Gamma likelihood"
 html_url: "https://github.com/JaxGaussianProcesses/GPJax/issues/298"
 user: "thomaspinder"

diff --git a/docs/_issues/2023-06-08-thomaspinder-GPJax-299.md b/docs/_issues/2023-06-08-thomaspinder-GPJax-299.md
@@ -1,5 +1,5 @@
 ---
-tags: ["bayesian-inference","enhancement","gaussian-processes","help-wanted","jax","machine-learning","probabilistic-programming"]
+tags: ["bayesian-inference","enhancement","gaussian-processes","help-wanted","jax","machine-learning","probabilistic-programming","stale"]
 title: "feat: Implement a multi-class discrete likelihood function."
 html_url: "https://github.com/JaxGaussianProcesses/GPJax/issues/299"
 user: "thomaspinder"

diff --git a/docs/_issues/2023-06-11-thomaspinder-GPJax-302.md b/docs/_issues/2023-06-11-thomaspinder-GPJax-302.md
@@ -1,5 +1,5 @@
 ---
-tags: ["bayesian-inference","enhancement","gaussian-processes","help-wanted","jax","machine-learning","probabilistic-programming","testing"]
+tags: ["bayesian-inference","enhancement","gaussian-processes","help-wanted","jax","machine-learning","probabilistic-programming","stale","testing"]
 title: "dev: Add non-conjugate smoke test"
 html_url: "https://github.com/JaxGaussianProcesses/GPJax/issues/302"
 user: "thomaspinder"

diff --git a/docs/_issues/2023-06-13-thomaspinder-GPJax-314.md b/docs/_issues/2023-06-13-thomaspinder-GPJax-314.md
@@ -1,5 +1,5 @@
 ---
-tags: ["bayesian-inference","enhancement","gaussian-processes","help-wanted","jax","machine-learning","probabilistic-programming"]
+tags: ["bayesian-inference","enhancement","gaussian-processes","help-wanted","jax","machine-learning","probabilistic-programming","stale"]
 title: "feat: Monte Carlo integrator."
 html_url: "https://github.com/JaxGaussianProcesses/GPJax/issues/314"
 user: "daniel-dodd"

diff --git a/docs/_issues/2023-06-13-thomaspinder-GPJax-315.md b/docs/_issues/2023-06-13-thomaspinder-GPJax-315.md
@@ -1,5 +1,5 @@
 ---
-tags: ["bayesian-inference","enhancement","gaussian-processes","help-wanted","jax","machine-learning","probabilistic-programming"]
+tags: ["bayesian-inference","enhancement","gaussian-processes","help-wanted","jax","machine-learning","probabilistic-programming","stale"]
 title: "feat: Poisson closed form expression for the variational expectation."
 html_url: "https://github.com/JaxGaussianProcesses/GPJax/issues/315"
 user: "daniel-dodd"

diff --git a/docs/_issues/2023-06-19-scikit-learn-scikit-learn-26617.md b/docs/_issues/2023-06-19-scikit-learn-scikit-learn-26617.md
diff --git a/docs/_issues/2024-02-01-idaholab-moose-26714.md b/docs/_issues/2024-02-01-idaholab-moose-26714.md
diff --git a/docs/_issues/2024-02-26-BradyAJohnston-MolecularNodes-440.md b/docs/_issues/2024-02-26-BradyAJohnston-MolecularNodes-440.md
@@ -0,0 +1,8 @@
+---
+tags: ["biochemistry","blender","blender-addon","enhancement","geometry-nodes","help-wanted","molecular","molecular-dynamics","molecular-graphics","molecular-modeling","molecule","pdb","protein","protein-data-bank","protein-structure","protein-visualization","proteins","sciart","structural-biology","visualisation"]
+title: "Add trajectory smoothing when importing via MDAnalysis"
+html_url: "https://github.com/BradyAJohnston/MolecularNodes/issues/440"
+user: "BradyAJohnston"
+repo: "BradyAJohnston/MolecularNodes"
+---
+
diff --git a/docs/_issues/2024-02-26-BradyAJohnston-MolecularNodes-441.md b/docs/_issues/2024-02-26-BradyAJohnston-MolecularNodes-441.md
@@ -0,0 +1,8 @@
+---
+tags: ["biochemistry","blender","blender-addon","enhancement","geometry-nodes","help-wanted","molecular","molecular-dynamics","molecular-graphics","molecular-modeling","molecule","pdb","protein","protein-data-bank","protein-structure","protein-visualization","proteins","sciart","structural-biology","visualisation"]
+title: "More options for MDAnalysis trajectory playback"
+html_url: "https://github.com/BradyAJohnston/MolecularNodes/issues/441"
+user: "BradyAJohnston"
+repo: "BradyAJohnston/MolecularNodes"
+---
+
diff --git a/docs/_issues/2024-04-01-BradyAJohnston-MolecularNodes-468.md b/docs/_issues/2024-04-01-BradyAJohnston-MolecularNodes-468.md
@@ -0,0 +1,8 @@
+---
+tags: ["biochemistry","blender","blender-addon","enhancement","geometry-nodes","help-wanted","molecular","molecular-dynamics","molecular-graphics","molecular-modeling","molecule","pdb","protein","protein-data-bank","protein-structure","protein-visualization","proteins","sciart","structural-biology","visualisation"]
+title: "Missing VDW radius values for rarely used elements"
+html_url: "https://github.com/BradyAJohnston/MolecularNodes/issues/468"
+user: "rbdavid"
+repo: "BradyAJohnston/MolecularNodes"
+---
+
diff --git a/docs/_issues/2024-05-01-dsavransky-EXOSIMS-372.md b/docs/_issues/2024-05-01-dsavransky-EXOSIMS-372.md
@@ -0,0 +1,8 @@
+---
+tags: ["bug"]
+title: "Small bug in dynamic completeness calculation"
+html_url: "https://github.com/dsavransky/EXOSIMS/issues/372"
+user: "turmon"
+repo: "dsavransky/EXOSIMS"
+---
+
diff --git a/docs/_issues/2024-06-18-plotly-dash-2894.md b/docs/_issues/2024-06-18-plotly-dash-2894.md
@@ -1,5 +1,5 @@
 ---
-tags: ["P3","bioinformatics","charting","dash","data-science","data-visualization","feature","finance","flask","gui-framework","jupyter","modeling","plotly","plotly-dash","productivity","python","react","rstats","technical-computing","web-app"]
+tags: ["P3","bioinformatics","charting","dash","dash-3.0","data-science","data-visualization","feature","finance","flask","gui-framework","jupyter","modeling","plotly","plotly-dash","productivity","python","react","rstats","technical-computing","web-app"]
 title: "Remove LogoutButton"
 html_url: "https://github.com/plotly/dash/issues/2894"
 user: "AnnMarieW"

diff --git a/docs/_issues/2024-06-24-dsavransky-EXOSIMS-380.md b/docs/_issues/2024-06-24-dsavransky-EXOSIMS-380.md
@@ -0,0 +1,8 @@
+---
+tags: ["bug","help-wanted"]
+title: "util/eccanom zero-size Exception"
+html_url: "https://github.com/dsavransky/EXOSIMS/issues/380"
+user: "turmon"
+repo: "dsavransky/EXOSIMS"
+---
+
diff --git a/docs/_issues/2024-07-26-PennyLaneAI-catalyst-964.md b/docs/_issues/2024-07-26-PennyLaneAI-catalyst-964.md
diff --git a/docs/_issues/2024-08-30-jupyterlab-jupyterlab-16734.md b/docs/_issues/2024-08-30-jupyterlab-jupyterlab-16734.md
@@ -0,0 +1,8 @@
+---
+tags: ["bug","jupyter","jupyterlab"]
+title: "Rename \"File Size\" column in file browser to \"Size\""
+html_url: "https://github.com/jupyterlab/jupyterlab/issues/16734"
+user: "JasonWeill"
+repo: "jupyterlab/jupyterlab"
+---
+
diff --git a/docs/_issues/2024-09-02-JuliaPlots-Makie.jl-4304.md b/docs/_issues/2024-09-02-JuliaPlots-Makie.jl-4304.md
@@ -0,0 +1,8 @@
+---
+tags: ["Makie","Observables","bug","gpu","graphics","julia","julia-language","plotting","visualization"]
+title: "Tracking plot types that don't yet have all `lift`s linked to the plot object"
+html_url: "https://github.com/MakieOrg/Makie.jl/issues/4304"
+user: "asinghvi17"
+repo: "JuliaPlots/Makie.jl"
+---
+
diff --git a/docs/_issues/2024-09-02-Pometry-Raphtory-1737.md b/docs/_issues/2024-09-02-Pometry-Raphtory-1737.md
@@ -0,0 +1,8 @@
+---
+tags: ["Good-first-issue","Python","Semantics/API","analytics","database","embedded-database","graph","graph-database","neo4j","olap","python","rust","temporal","time-series"]
+title: "Add an `import_as` function for edges and nodes"
+html_url: "https://github.com/Pometry/Raphtory/issues/1737"
+user: "miratepuffin"
+repo: "Pometry/Raphtory"
+---
+
diff --git a/docs/_issues/2024-09-03-JuliaPlots-Makie.jl-4308.md b/docs/_issues/2024-09-03-JuliaPlots-Makie.jl-4308.md
@@ -0,0 +1,8 @@
+---
+tags: ["bug","gpu","graphics","help-wanted","julia","julia-language","plotting","visualization"]
+title: "Precompilation warnings"
+html_url: "https://github.com/MakieOrg/Makie.jl/issues/4308"
+user: "ufechner7"
+repo: "JuliaPlots/Makie.jl"
+---
+
diff --git a/docs/_issues/2024-09-04-pandas-dev-pandas-59712.md b/docs/_issues/2024-09-04-pandas-dev-pandas-59712.md
@@ -0,0 +1,8 @@
+---
+tags: ["Bug","Groupby","Reduction-Operations","alignment","data-analysis","data-science","flexible","pandas","python"]
+title: "BUG: groupby().any() returns True instead of False for groups where timedelta column is all null"
+html_url: "https://github.com/pandas-dev/pandas/issues/59712"
+user: "sfc-gh-mvashishtha"
+repo: "pandas-dev/pandas"
+---
+
diff --git a/docs/_issues/2024-09-05-qutip-qutip-2524.md b/docs/_issues/2024-09-05-qutip-qutip-2524.md
@@ -0,0 +1,8 @@
+---
+tags: ["DOC","python","quantum","quantum-computing","quantum-information","quantum-mechanics","quantum-optics","quantum-toolbox","qutip","unitaryhack"]
+title: "Family packages in main documentation"
+html_url: "https://github.com/qutip/qutip/issues/2524"
+user: "pmenczel"
+repo: "qutip/qutip"
+---
+
diff --git a/docs/_issues/2024-09-07-InsightSoftwareConsortium-ITK-4838.md b/docs/_issues/2024-09-07-InsightSoftwareConsortium-ITK-4838.md
@@ -0,0 +1,8 @@
+---
+tags: ["Good-first-issue","cpp","hacktoberfest","image-analysis","insight-toolkit","itk","medical-imaging","numfocus","open-science","open-source","python","reproducible-research","scientific-computing","typeDocumentation"]
+title: "Make ITK keywords in PyPI consistent"
+html_url: "https://github.com/InsightSoftwareConsortium/ITK/issues/4838"
+user: "jhlegarreta"
+repo: "InsightSoftwareConsortium/ITK"
+---
+
diff --git a/docs/_issues/2024-09-07-xgi-org-xgi-585.md b/docs/_issues/2024-09-07-xgi-org-xgi-585.md
@@ -0,0 +1,8 @@
+---
+tags: ["documentation","higher-order","higher-order-networks","hypergraphs","network-science"]
+title: "add dark version of logo to online docs"
+html_url: "https://github.com/xgi-org/xgi/issues/585"
+user: "maximelucas"
+repo: "xgi-org/xgi"
+---
+