diff --git a/.github/dependabot.yml b/.github/dependabot.yml
index 08c3106..7ce9081 100644
--- a/.github/dependabot.yml
+++ b/.github/dependabot.yml
@@ -21,3 +21,13 @@ updates:
           - "github/*"
     schedule:
       interval: "weekly"
+
+  - package-ecosystem: pip
+    directory: /papers/P2988
+    schedule:
+      interval: daily
+
+  - package-ecosystem: pip
+    directory: /
+    schedule:
+      interval: daily
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 31c1dbb..3fa22b1 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -11,8 +11,14 @@ on:
   permissions:
     contents: read
 
+permissions:
+  contents: read
+
 jobs:
   build:
+    permissions:
+      checks: write  # for coverallsapp/github-action to create new checks
+      contents: read  # for actions/checkout to fetch code
     name: ${{ matrix.config.name }}
     runs-on: ubuntu-24.04
     container:
@@ -31,7 +37,12 @@ jobs:
           - {name: "Ubuntu GCC 13", tag: "gcc:13", toolchain: "gcc-13",  cmake_args: "-G \"Ninja Multi-Config\" -DCMAKE_CONFIGURATION_TYPES=\"RelWithDebInfo;Asan\"  	-DCMAKE_PREFIX_PATH=\"./infra/cmake\" "}
           - {name: "Ubuntu GCC 12", tag: "gcc:12", toolchain: "gcc-12",  cmake_args: "-G \"Ninja Multi-Config\" -DCMAKE_CONFIGURATION_TYPES=\"RelWithDebInfo;Asan\"  	-DCMAKE_PREFIX_PATH=\"./infra/cmake\" "}
     steps:
-      - uses: actions/checkout@v6
+      - name: Harden the runner (Audit all outbound calls)
+        uses: step-security/harden-runner@20cf305ff2072d973412fa9b1e3a4f227bda3c76 # v2.14.0
+        with:
+          egress-policy: audit
+
+      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
         with:
           submodules: 'true'
         # If Clang 17, install a newer version of libc++ and libc++abi.
@@ -104,7 +115,7 @@ jobs:
           cmake --build .build --config Gcov --target process_coverage -- -k 0
       - name: Coveralls
         if: matrix.config.coverage
-        uses: coverallsapp/github-action@main
+        uses: coverallsapp/github-action@ba6dae83310bbd6d33ff77092650dc40bd444a2a # main
         with:
           file: .build/coverage.json
           github-token: ${{ secrets.GITHUB_TOKEN }}
@@ -118,7 +129,12 @@ jobs:
       issues: write
     steps:
       # See https://github.com/cli/cli/issues/5075
-      - uses: actions/checkout@v6
+      - name: Harden the runner (Audit all outbound calls)
+        uses: step-security/harden-runner@20cf305ff2072d973412fa9b1e3a4f227bda3c76 # v2.14.0
+        with:
+          egress-policy: audit
+
+      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
       - name: Create issue
         run: |
           issue_num=$(gh issue list -s open -S "[SCHEDULED-BUILD] Build & Test failure" -L 1 --json number | jq 'if length == 0 then -1 else .[0].number end')
diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
index a1ac81b..9bad9d7 100644
--- a/.github/workflows/codeql.yml
+++ b/.github/workflows/codeql.yml
@@ -58,6 +58,11 @@ jobs:
         # If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how
         # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages
     steps:
+      - name: Harden the runner (Audit all outbound calls)
+        uses: step-security/harden-runner@20cf305ff2072d973412fa9b1e3a4f227bda3c76 # v2.14.0
+        with:
+          egress-policy: audit
+
       - name: Checkout repository
         uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
diff --git a/.github/workflows/doxygen-gh-pages.yml b/.github/workflows/doxygen-gh-pages.yml
index 8b107a3..d8cb6fe 100644
--- a/.github/workflows/doxygen-gh-pages.yml
+++ b/.github/workflows/doxygen-gh-pages.yml
@@ -6,13 +6,21 @@ on:
       - main
       - doxify
 
+permissions:
+  contents: read
+
 jobs:
   deploy:
     runs-on: ubuntu-latest
     permissions:
       contents: write
     steps:
-      - uses: DenverCoder1/doxygen-github-pages-action@v2.0.0
+      - name: Harden the runner (Audit all outbound calls)
+        uses: step-security/harden-runner@20cf305ff2072d973412fa9b1e3a4f227bda3c76 # v2.14.0
+        with:
+          egress-policy: audit
+
+      - uses: DenverCoder1/doxygen-github-pages-action@a30f9538f8ef1305aeceb563018f452c7a62d200 # v2.0.0
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           branch: gh-pages
diff --git a/.github/workflows/ossf-scorecard-analysis.yml b/.github/workflows/ossf-scorecard-analysis.yml
index 0c0ba08..644ba49 100644
--- a/.github/workflows/ossf-scorecard-analysis.yml
+++ b/.github/workflows/ossf-scorecard-analysis.yml
@@ -21,6 +21,11 @@ jobs:
       id-token: write
 
     steps:
+      - name: Harden the runner (Audit all outbound calls)
+        uses: step-security/harden-runner@20cf305ff2072d973412fa9b1e3a4f227bda3c76 # v2.14.0
+        with:
+          egress-policy: audit
+
       - name: "Checkout code"
         uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
         with:
diff --git a/.github/workflows/pre-commit-update.yml b/.github/workflows/pre-commit-update.yml
index 6809c36..4f02dac 100644
--- a/.github/workflows/pre-commit-update.yml
+++ b/.github/workflows/pre-commit-update.yml
@@ -7,6 +7,9 @@ on:
   schedule:
     - cron: "0 16 * * 0"
 
+permissions:
+  contents: read
+
 jobs:
   auto-update-pre-commit:
     permissions:
diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
index 8dd28a3..4501740 100644
--- a/.github/workflows/pre-commit.yml
+++ b/.github/workflows/pre-commit.yml
@@ -5,6 +5,9 @@ on:
   pull_request:
   push:
 
+permissions:
+  contents: read
+
 jobs:
   pre-commit-push:
     name: Pre-Commit check on Push
@@ -15,11 +18,16 @@ jobs:
       contents: read
 
     steps:
+      - name: Harden the runner (Audit all outbound calls)
+        uses: step-security/harden-runner@20cf305ff2072d973412fa9b1e3a4f227bda3c76 # v2.14.0
+        with:
+          egress-policy: audit
+
       - name: Checkout repository
-        uses: actions/checkout@v6
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
 
       - name: Set up Python
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6.1.0
         with:
           python-version: 3.13
 
@@ -27,7 +35,7 @@ jobs:
         # only made in the push commit.
         #
         # So linting error persists when there's formatting problem.
-      - uses: pre-commit/action@v3.0.1
+      - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1
 
   pre-commit-pr:
     name: Pre-Commit check on PR
@@ -41,8 +49,13 @@ jobs:
       pull-requests: write
 
     steps:
+      - name: Harden the runner (Audit all outbound calls)
+        uses: step-security/harden-runner@20cf305ff2072d973412fa9b1e3a4f227bda3c76 # v2.14.0
+        with:
+          egress-policy: audit
+
       - name: Checkout repository
-        uses: actions/checkout@v6
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
 
         # pull_request_target checkout the base of the repo
         # We need to checkout the actual pr to lint the changes.
@@ -52,16 +65,16 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Set up Python
-        uses: actions/setup-python@v6
+        uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6.1.0
         with:
           python-version: 3.13
 
         # we only lint on the changed file in PR.
       - name: Get Changed Files
         id: changed-files
-        uses: step-security/changed-files@v46
+        uses: step-security/changed-files@95b56dadb92a30ca9036f16423fd3c088a71ee94 # v46.0.5
 
-      - uses: pre-commit/action@v3.0.1
+      - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1
         id: run-pre-commit
         with:
           extra_args: --files ${{ steps.changed-files.outputs.all_changed_files }}