fix: tighten workflow permissions, add security hardening, and fix uv tool invocations

## What

Move elevated permissions from workflow level to job level across three workflows
(mark-ready-when-ready, scorecard, stale) so each job only holds the permissions it
actually needs. Add step-security/harden-runner to all eight workflows that define steps.
Add CodeQL SAST scanning and dependency-review workflows. Add pre-commit configuration
with gitleaks, formatting hooks, and local linter hooks. Fix Makefile to invoke flake8,
pytest, pylint, and mypy via `uv run python -m` since they lack console script entry
points in the uv venv. Upgrade PyJWT from 2.11.0 to 2.12.1 to address CVE-2026-32597.

## Why

Workflow-level write permissions apply to every job in the workflow, granting broader
access than necessary. Moving them to job level follows the principle of least privilege.
Harden-runner audits outbound network calls from GitHub-hosted runners, improving
supply-chain visibility. CodeQL and dependency-review close gaps in static analysis and
vulnerable-dependency detection. The Makefile commands failed under uv because those
packages don't install console scripts; `python -m` ensures the tools are always found.
PyJWT <= 2.11.0 doesn't validate the RFC 7515 `crit` header parameter (CVSS 7.5).

## Notes

- The `uv run` to `uv run python -m` change also affects CI since python-ci calls `make lint` and `make test`
- release.yml, auto-labeler.yml, and pr-title.yml use reusable workflows at the job level so harden-runner cannot be added there; it must go in the reusable workflow definitions instead
- The scorecard workflow previously used `permissions: read-all` which granted read access to all scopes; now explicitly scoped to only what's needed
- PyJWT is a transitive dependency; verify downstream consumers aren't relying on the old crit-header-ignored behavior

Signed-off-by: jmeridth <jmeridth@gmail.com>

Author: jmeridth

.github/copilot-instructions.md

@@ -16,10 +16,8 @@ This is a GitHub Action that given an organization or specified repositories, pr
 ## Repository Structure
 
 - `Makefile`: Contains commands for linting, testing, and other tasks
-- `requirements.txt`: Python dependencies for the project
-- `requirements-test.txt`: Python dependencies for testing
+- `pyproject.toml`: Python dependencies and project configuration
 - `README.md`: Project documentation and setup instructions
-- `setup.py`: Python package setup configuration
 - `test_*.py`: Python test files matching the naming convention for test discovery
 
 ## Key Guidelines

.github/workflows/codeql.yml

@@ -0,0 +1,77 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: ["main"]
+  schedule:
+    - cron: "0 0 * * 1"
+
+permissions:
+  contents: read
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: ["python"]
+        # CodeQL supports [ $supported-codeql-languages ]
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+      - name: Harden the runner (Audit all outbound calls)
+        uses: step-security/harden-runner@58077d3c7e43986b6b15fba718e8ea69e387dfcc # v2.15.1
+        with:
+          egress-policy: audit
+
+      - name: Checkout repository
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          persist-credentials: false
+
+      # Initializes the CodeQL tools for scanning.
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@820e3160e279568db735cee8ed8f8e77a6da7818 # v3.32.6
+        with:
+          languages: ${{ matrix.language }}
+          # If you wish to specify custom queries, you can do so here or in a config file.
+          # By default, queries listed here will override any specified in a config file.
+          # Prefix the list here with "+" to use these queries and those in the config file.
+
+      # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+      # If this step fails, then you should remove it and run the build manually (see below)
+      - name: Autobuild
+        uses: github/codeql-action/autobuild@820e3160e279568db735cee8ed8f8e77a6da7818 # v3.32.6
+
+      # If the Autobuild fails above, remove it and uncomment the following three lines.
+      #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
+
+      # - run: |
+      #   echo "Run, Build Application using script"
+      #   ./location_of_script_within_repo/buildscript.sh
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@820e3160e279568db735cee8ed8f8e77a6da7818 # v3.32.6
+        with:
+          category: "/language:${{matrix.language}}"

.github/workflows/contributors_report.yaml

@@ -16,6 +16,11 @@ jobs:
       issues: write
 
     steps:
+      - name: Harden the runner (Audit all outbound calls)
+        uses: step-security/harden-runner@58077d3c7e43986b6b15fba718e8ea69e387dfcc # v2.15.1
+        with:
+          egress-policy: audit
+
       - name: Get dates for last month
         shell: bash
         run: |

.github/workflows/copilot-setup-steps.yml

@@ -25,6 +25,11 @@ jobs:
     # You can define any steps you want, and they will run before the agent starts.
     # If you do not check out your code, Copilot will do this for you.
     steps:
+      - name: Harden the runner (Audit all outbound calls)
+        uses: step-security/harden-runner@58077d3c7e43986b6b15fba718e8ea69e387dfcc # v2.15.1
+        with:
+          egress-policy: audit
+
       - name: Checkout code
         uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:

.github/workflows/dependency-review.yml

@@ -0,0 +1,29 @@
+# Dependency Review Action
+#
+# This Action will scan dependency manifest files that change as part of a Pull Request,
+# surfacing known-vulnerable versions of the packages declared or updated in the PR.
+# Once installed, if the workflow run is marked as required,
+# PRs introducing known-vulnerable packages will be blocked from merging.
+#
+# Source repository: https://github.com/actions/dependency-review-action
+name: "Dependency Review"
+on: [pull_request]
+
+permissions:
+  contents: read
+
+jobs:
+  dependency-review:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Harden the runner (Audit all outbound calls)
+        uses: step-security/harden-runner@58077d3c7e43986b6b15fba718e8ea69e387dfcc # v2.15.1
+        with:
+          egress-policy: audit
+
+      - name: "Checkout Repository"
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          persist-credentials: false
+      - name: "Dependency Review"
+        uses: actions/dependency-review-action@2031cfc080254a8a887f58cffee85186f0e49e48 # v4.9.0

.github/workflows/docker-ci.yml

@@ -14,6 +14,11 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
+      - name: Harden the runner (Audit all outbound calls)
+        uses: step-security/harden-runner@58077d3c7e43986b6b15fba718e8ea69e387dfcc # v2.15.1
+        with:
+          egress-policy: audit
+
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:
           persist-credentials: false

.github/workflows/mark-ready-when-ready.yml

@@ -5,10 +5,7 @@ on:
     types: [opened, edited, labeled, unlabeled, synchronize]
 
 permissions:
-  checks: read
-  contents: write
-  pull-requests: write
-  statuses: read
+  contents: read
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number }}
@@ -18,10 +15,20 @@ jobs:
   mark-ready:
     name: Mark as ready after successful checks
     runs-on: ubuntu-latest
+    permissions:
+      checks: read
+      contents: write
+      pull-requests: write
+      statuses: read
     if: |
       contains(github.event.pull_request.labels.*.name, 'Mark Ready When Ready') &&
       github.event.pull_request.draft == true
     steps:
+      - name: Harden the runner (Audit all outbound calls)
+        uses: step-security/harden-runner@58077d3c7e43986b6b15fba718e8ea69e387dfcc # v2.15.1
+        with:
+          egress-policy: audit
+
       - name: Mark ready when ready
         uses: kenyonj/mark-ready-when-ready@33b13c51ba23786efb933701ef253352baf05bdd # main (contents:write fix)
         with:

.github/workflows/python-ci.yml

@@ -24,6 +24,11 @@ jobs:
       matrix:
         python-version: [3.11, 3.12, 3.13, 3.14]
     steps:
+      - name: Harden the runner (Audit all outbound calls)
+        uses: step-security/harden-runner@58077d3c7e43986b6b15fba718e8ea69e387dfcc # v2.15.1
+        with:
+          egress-policy: audit
+
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:
           persist-credentials: false

.github/workflows/scorecard.yml

@@ -13,17 +13,24 @@ on:
   push:
     branches: [main]
 
-permissions: read-all
+permissions:
+  contents: read
 
 jobs:
   analysis:
     name: Merge to Main Scorecard analysis
     runs-on: ubuntu-latest
     permissions:
+      contents: read
       security-events: write
       id-token: write
 
     steps:
+      - name: Harden the runner (Audit all outbound calls)
+        uses: step-security/harden-runner@58077d3c7e43986b6b15fba718e8ea69e387dfcc # v2.15.1
+        with:
+          egress-policy: audit
+
       - name: "Checkout code"
         uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:

.github/workflows/stale.yml

@@ -4,13 +4,20 @@ on:
     - cron: "30 1 * * *"
 
 permissions:
-  issues: write
-  pull-requests: read
+  contents: read
 
 jobs:
   stale:
     runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: read
     steps:
+      - name: Harden the runner (Audit all outbound calls)
+        uses: step-security/harden-runner@58077d3c7e43986b6b15fba718e8ea69e387dfcc # v2.15.1
+        with:
+          egress-policy: audit
+
       - uses: actions/stale@b5d41d4e1d5dceea10e7104786b73624c18a190f # v10.2.0
         with:
           stale-issue-message: "This issue is stale because it has been open 21 days with no activity. Remove stale label or comment or this will be closed in 14 days."