security: SHA-pin all Actions, harden release pipeline, add pin verification (#824)

* security: SHA-pin all Actions, harden release pipeline, add pin verification

Hardens the CI/CD supply chain against the LiteLLM/Trivy-style attack (a
compromised third-party Action with a mutable tag stealing a long-lived
publishing token) and closes several related gaps found in an audit of the
actual repository state.

- Pin every third-party GitHub Action across all workflows to a full commit
  SHA (tag kept as a trailing comment); add verify-action-pins.yml, a CI
  check that confirms via the GitHub API that each pin still matches its
  tag, on every workflow change, push to main, and weekly.
- Scope release.yml permissions to the job level (workflow defaults to
  contents: read); add a concurrency group so simultaneous tag pushes can't
  race the publish job.
- Add SLSA build provenance attestation (actions/attest-build-provenance)
  for every released wheel.
- Fix a latent bug in security-scan.yml: the PR-comment step was missing
  pull-requests: write and silently failing; add bounded artifact retention
  for uploaded scan reports.
- Group github-actions Dependabot updates to cut review noise.
- Document the resulting posture in SECURITY.md for auditors/regulated
  adopters, including what's enforced and what a fork needs to reconfigure
  for itself (environment/branch protection, Trusted Publishing trust).

Also (via GitHub API, not in this diff): created a protected `pypi`
environment with a required reviewer restricted to v* tags, and enabled
branch protection on main (required review, required status checks, no
force-push/deletion).

* fix: harden verify-action-pins per PR #824 bot review

Addresses real findings from the automated review on #824:

- The script previously only matched uses: lines that already contained a
  40-hex SHA, so a newly added mutable-tag action (e.g. some/action@v1)
  would never be scanned at all and the check would pass silently. It now
  matches every uses: line and hard-fails on any ref that isn't a full
  commit SHA.
- A tag that fails to resolve via the GitHub API (rate limit, deleted tag)
  previously only logged a warning and continued; that's now a hard
  failure too, since an unverifiable pin is exactly the failure mode this
  check exists to catch.
- verify-action-pins.yml only triggered on .github/workflows/** changes,
  so an edit to the verifier script itself wouldn't run the check that
  verifies it. Added the script path to both trigger filters.

The reviewer's claim that slash-containing tag comments (release/v1) break
the API lookup did not reproduce - tested directly against
pypa/gh-action-pypi-publish@release/v1 and GitHub's commits API resolves
multi-segment refs natively - so no change was needed there.

Verified with a synthetic test workflow containing a mutable-tag action,
a correctly-pinned SHA, and a deliberately mismatched SHA: the updated
script now catches the first and third cases and passes the second. Also
re-ran against the real workflow tree (40/40 pins still verify clean).

* fix: repair broken Safety scan and PR comment formatting

The "Comment PR with Security Results" step was producing garbled output
(literal \n characters instead of newlines, "undefined:" labels) because:

- Every line in the JS comment builder used \n (escaped backslash-n)
  inside template literals, which JS renders as the literal two-character
  string \n, not a newline.
- The Semgrep section read issue.rule_id, but Semgrep's JSON field is
  check_id - hence "undefined: <path>" for every entry.

Rewrote the comment builder to construct each section as an array of
lines joined with a real '\n', with correct field names, and collapsed
long finding lists into a <details> block instead of a flat list.
Verified by extracting the exact script and running it under node against
synthetic fixtures matching each tool's real JSON schema (found/clean/
missing-report paths all render correctly).

While tracing the "undefined" and always-empty Safety section, found the
Safety step itself was silently broken:

- `safety check --json --output safety-report.json` is invalid in
  Safety 3.x: --output now selects a console format (json/text/screen),
  not a file path. The command errored on every run (swallowed by
  `|| true`), so safety-report.json was never created and the PR comment
  always fell back to a generic "scan completed" message. Switched to
  `--save-json`, which is the correct flag for writing a JSON report to
  disk, and confirmed against the real safety 3.8.1 CLI locally.
- Even with a report, the code read vuln.package - the real field is
  package_name.
- The job never installed Semantica's own dependencies before scanning,
  so `safety check` (which defaults to scanning the environment) was
  auditing the scanner tools' own dependencies, not Semantica's. Added
  `pip install -e ".[llm-litellm]"` so the project's actual dependency
  tree - including the LiteLLM extra this whole hardening effort is
  about - is what gets scanned.

Also updated the corresponding SECURITY.md bullet to describe what Safety
actually covers now.

* fix: remove unused pypdf2 dependency (CVE-2023-36464)

Now that the Safety scan step actually runs (see previous commit), it
correctly failed this PR's checks on CVE-2023-36464 in pypdf2==3.0.1 - a
real, pre-existing vulnerability that was invisible until the scan was
fixed.

PyPDF2 is not a patchable dependency here: the project is discontinued
(merged into `pypdf`), 3.0.1 is its final release, and there is no fixed
version to upgrade to. Grepping the repo for `import PyPDF2` / `from
PyPDF2` turns up nothing - it was never actually imported anywhere. Its
only presence outside pyproject.toml was in docstrings describing a
"PyPDF2.PdfReader() fallback" for PDF parsing that was never implemented
in code; pdfplumber is the library actually used. Removed the dependency
and corrected the stale docstrings in parse/__init__.py, parse/methods.py,
parse/pdf_parser.py, and ingest/email_ingestor.py accordingly.

* fix: suppress Bandit B324 false positives on non-cryptographic MD5 use

Same pattern as the previous pypdf2 commit: fixing the Safety scan
surfaced this PR's own Bandit HIGH-severity gate actually blocking on 10
pre-existing findings, all Bandit B324 ("Use of weak MD5 hash for
security").

Checked each of the 10 call sites: every one uses hashlib.md5() to build
a short deterministic cache key, entity ID, or IRI suffix from already-
non-secret input (query text, entity text/type, class/property names) -
none are used for passwords, tokens, or integrity verification of
untrusted data. This is exactly the case Bandit's own message points at
("Consider usedforsecurity=False").

Did not use usedforsecurity=False itself: that keyword argument was
added to hashlib in Python 3.9, and pyproject.toml declares
`requires-python = ">=3.8"` - adding it unconditionally risks a TypeError
on 3.8. Used a targeted `# nosec B324` comment with a one-line
justification instead, which suppresses only this specific check and
carries no runtime behavior change on any supported Python version.

Verified locally: bandit -r semantica/ -ll now reports 0 HIGH-severity
findings (was 10).

* docs: add CHANGELOG entry for #824 CI/CD supply-chain hardening

Covers the SHA-pinning + verify-action-pins.yml enforcement, release.yml
hardening (job-scoped permissions, concurrency, SLSA provenance), the
pypi environment/branch protection GitHub-side config, the
security-scan.yml Safety/comment-formatting fixes, and the two
vulnerabilities those fixes surfaced (pypdf2 CVE-2023-36464 removal,
Bandit B324 suppression).

* fix: close two remaining gaps missed by upstream bot-review fixes

verify-action-pins.sh:
- Quoted uses: lines (e.g. uses: owner/action@SHA) were not matched
  by the existing regex, so a SHA-pinned action written with quotes would
  silently skip verification. Updated the main ERE to accept an optional
  leading/trailing single or double quote around the owner/action@ref
  value, and excluded quote chars from the inner character classes so the
  ref is still extracted cleanly.
- The grep input glob only covered *.yml. GitHub also treats *.yaml as a
  valid workflow extension. Added *.yaml to the glob and a 2>/dev/null
  guard so the command doesn't fail when no *.yaml files exist.

security-scan.yml (on top of Kaif's --save-json fix in 67c7ec2a):
- Kaif's fix kept the '|| echo 0' fallback on the VULNS= line, so all
  five scanner-failure modes (file missing, empty file, malformed JSON,
  valid JSON with no 'vulnerabilities' key, vulnerabilities: null) still
  silently produce VULNS=0 or VULNS=null and pass the merge-blocker check.
- Added guard 1: '[ ! -s safety-report.json ]' fails loudly if Safety
  crashed before writing a report (covers missing and empty-file cases).
- Dropped the '|| echo 0' fallback and added guard 2: '[[ ! VULNS =~
  ^[0-9]+$ ]]' fails loudly on non-integer VULNS (covers malformed JSON,
  missing key, and null cases). Both guards emit ::error:: annotations.
- Verified with a 7-case simulation: all 5 failure modes now exit 1;
  genuine zero-vuln and real-vuln cases still behave correctly.

* fix: correct bash [[ =~ ]] quoting that broke verify-action-pins.sh in CI

The regex for matching uses: lines was embedded directly inline in a
[[ =~ ]] test with literal \" and \' escape sequences. Bash's conditional-
expression parser interprets these as shell syntax rather than regex
literals, producing:

  syntax error in conditional expression: unexpected token ')'

at line 27 on every CI run.

Fix: move the regex into a USES_PATTERN variable using safe single-quote
shell-string concatenation so the [[ =~ ]] parser receives an unquoted
variable reference ($USES_PATTERN) rather than a literal pattern containing
bash-special characters. The regex semantics are identical: optional
leading/trailing quote around owner/action@ref, quote chars excluded from
capture groups.

Verified in real bash 5.2.21 (Git for Windows):
  No syntax error on the real 40-pin workflow tree (Checked 40)
  Unquoted SHA pin:      MATCH, correct repo+ref extracted
  Double-quoted SHA pin: MATCH, correct repo+ref extracted
  Single-quoted SHA pin: MATCH, correct repo+ref extracted
  .yaml extension file:  MATCH, correct repo+ref extracted
  ./local-action:        NO MATCH (correct)
  docker://:             NO MATCH (correct)

* docs: add 3 missing items to fork-reconfiguration checklist in SECURITY.md

The checklist covered Trusted Publishing trust, protected environment,
branch protection, and Dependabot github-actions entry. Three non-forking
controls described elsewhere in SECURITY.md were omitted:

- GitHub secret scanning and push protection (repo settings, not copied
  on fork)
- GitGuardian (GitHub App installation scoped to this specific repo,
  requires separate install on any fork)
- CodeQL Default Setup vs Advanced Setup state (repo setting that affects
  whether the upload-sarif step in codeql.yml does anything)

Added as items 5, 6, 7 matching the existing numbered bullet style.

* fix: update github/codeql-action pins to v4 tip (SHA drift caught by verify check)

verify-action-pins caught that github/codeql-action@v4 tag was re-pointed
upstream:

  old: f205ea1c3313d32999d8d6a48b4f6530d4437b38
  new: d1ba80a13dd99fba24a470575428917156a28b43

Updated all 8 occurrences across codeql.yml (init x3, autobuild, analyze,
upload-sarif) and defender-for-devops.yml (upload-sarif x2). Tag comment
# v4 unchanged — the tag itself hasn't changed, only what commit it points to.

---------

Co-authored-by: Sameer6305 <sskadam6305@gmail.com>

SECURITY.md

@@ -112,6 +112,101 @@ We regularly update dependencies to address security vulnerabilities. However, y
 - Be cautious with external API calls
 - Implement proper authentication and authorization
 
+## CI/CD Supply-Chain Security
+
+Semantica's build and release pipeline is explicitly hardened against
+CI/CD supply-chain attacks — the class of attack behind the March 2026
+LiteLLM/Trivy incident, where a compromised third-party Action with a
+**mutable tag** was used to steal a long-lived publishing token, after which
+malicious packages were pushed straight to PyPI without ever touching the
+source repository. Every control below maps directly to closing one step of
+that attack chain.
+
+### Immutable build inputs
+
+- **Risk**: a tag (`@v4`, `@release/v1`) is re-pointed by a compromised upstream maintainer or account, silently changing what every consumer's CI runs.
+  **Control**: every third-party GitHub Action in every workflow is pinned to a full 40-character commit SHA, with the human-readable tag kept only as a trailing comment (e.g. `actions/checkout@3d3c42e... # v7`).
+- **Risk**: a SHA pin drifts out of sync with its own comment over time, or is mistyped.
+  **Control**: `verify-action-pins.yml` fails closed on any `uses:` reference that isn't a full commit SHA (catching a newly added mutable tag, not just auditing existing pins), resolves every pinned tag via the GitHub API on each workflow change, on every push to `main`, and weekly, and fails if the SHA no longer matches the tag it claims to be — an API lookup that can't be resolved is treated as a failure, not a silent skip.
+- **Risk**: manually re-pinning ~15 actions across 8 workflow files on every upstream release is error-prone.
+  **Control**: Dependabot (`github-actions` ecosystem) opens a grouped PR that bumps the SHA *and* the tag comment together whenever an action releases — pins never require hand-editing.
+
+### Publishing pipeline (highest-privilege path)
+
+- **Risk**: a long-lived `PYPI_TOKEN` sitting in repo/org secrets is exfiltrated by any compromised step.
+  **Control**: PyPI publishing uses Trusted Publishing (OIDC) (`id-token: write`) — there is no long-lived PyPI credential anywhere in this repository to steal.
+- **Risk**: a compromised CI run publishes to PyPI with no human in the loop.
+  **Control**: the publish job runs only inside a protected `pypi` GitHub Environment with a required human reviewer — every release needs manual approval in the Actions UI before it runs.
+- **Risk**: the release job could be triggered from an arbitrary branch/ref.
+  **Control**: the `pypi` environment's deployment-branch policy is restricted to `v*` tags only.
+- **Risk**: a scanner or unrelated job inherits publish-level credentials.
+  **Control**: `release.yml` sets `permissions: contents: read` at the workflow level; `contents: write` / `id-token: write` / `attestations: write` are granted only to the release job, never workflow-wide.
+- **Risk**: two tag pushes race through the publish pipeline simultaneously.
+  **Control**: `concurrency: group: release-${{ github.ref }}` serializes releases per tag.
+- **Risk**: a consumer can't verify a wheel on PyPI actually came from this repo's CI.
+  **Control**: SLSA build provenance is attested for every release via `actions/attest-build-provenance`, producing a signed, verifiable record of the exact commit and workflow run that produced the artifact (checkable with `gh attestation verify`).
+
+### Repository controls
+
+- **Risk**: unreviewed or force-pushed changes land on `main`.
+  **Control**: `main` requires 1 approving PR review (stale approvals dismissed on new pushes), resolved conversations, and blocks force-pushes and branch deletion.
+- **Risk**: a PR merges without its security/CI checks passing.
+  **Control**: merges require the `build`, `Analyze Python` (CodeQL), and `security-scan` checks to pass, in strict mode (checks must be re-run against the latest `main`).
+- **Risk**: a compromised scanner job reaches secrets or write access.
+  **Control**: scanning jobs (`CodeQL`, `security-scan.yml`, `security.yml`, `defender-for-devops.yml`) run with read-only, least-privilege permissions (typically `contents: read` + `security-events: write` only) and never share a job, environment, or secret scope with the publish job.
+- **Risk**: secrets are committed accidentally.
+  **Control**: GitHub secret scanning and push protection are both enabled at the repository level, rejecting pushes that contain recognizable credential patterns before they land in history.
+
+## Automated Security Scanning
+
+Every scan below runs continuously in CI, not just at release time:
+
+- **CodeQL** (`security-and-quality` query pack) — Python source: injection, unsafe deserialization, and other code-level vulnerability classes. Runs in `codeql.yml` on every push/PR to `main` and weekly.
+- **Bandit** — Python-specific security anti-patterns (hardcoded secrets, unsafe `eval`/`pickle`, weak crypto, etc.); CI fails on any HIGH-severity finding. Runs in `security-scan.yml` on every push/PR to `main` and twice weekly.
+- **Semgrep** (`p/security` ruleset) — cross-language static-analysis security patterns. Runs in `security-scan.yml` on every push/PR to `main` and twice weekly.
+- **Safety** — known CVEs in Semantica's own installed dependencies, including optional LLM-provider extras such as LiteLLM; CI fails on any match. Runs in `security-scan.yml` on every push/PR to `main` and twice weekly.
+- **pip-audit** — independent, PyPA-maintained vulnerability database cross-check against installed dependencies (Safety and pip-audit use different advisory sources, so both run). Runs in `security.yml` weekly.
+- **Microsoft Defender for DevOps** (`eslint`, `templateanalyzer`, `terrascan`) — JavaScript/TypeScript lint-security rules and infrastructure-as-code misconfigurations. Runs in `defender-for-devops.yml` on every push/PR to `main` and weekly.
+- **Checkov** — Kubernetes, Helm, Dockerfile, GitHub Actions, and secrets-pattern IaC scanning; results upload to the same Security tab as CodeQL. Runs in `defender-for-devops.yml` on every push/PR to `main` and weekly.
+- **GitGuardian** — secret-detection check on every pull request, installed as a GitHub App integration (not a repo-local workflow). Runs on every PR.
+- **GitHub secret scanning + push protection** — blocks known credential patterns before they're pushed, and continuously scans existing history. Platform-level, continuous.
+- **Dependabot** — version/security PRs for Python, Docker, and GitHub Actions dependencies, grouped where relevant to reduce review noise. Configured in `.github/dependabot.yml`, runs weekly for security-relevant packages and monthly for docs dependencies.
+- **`verify-action-pins.yml`** — enforces that every Action reference is a full commit SHA (failing on a newly introduced mutable tag) and confirms each SHA still matches the tag it claims to be. Runs on every workflow change, every push to `main`, and weekly.
+
+All SARIF-producing scanners (CodeQL, Checkov, Microsoft Defender) publish
+findings to the repository's **Security → Code scanning alerts** tab, giving
+a single audit trail across tools rather than scattered per-tool reports.
+
+### Adopting this posture in a fork or downstream deployment
+
+Teams standing up their own instance of Semantica, or forking it for an
+internal/regulated deployment, can reuse this posture directly:
+
+1. Keep Dependabot's `github-actions` ecosystem entry — it is what keeps
+   SHA pins current without manual maintenance.
+2. Re-run `verify-action-pins.yml` after re-pointing the repository's Actions
+   at your own mirrors, if you do so.
+3. If you publish your own PyPI package from a fork, configure your own
+   Trusted Publishing trust relationship on PyPI (Trusted Publishing is
+   scoped to a specific `owner/repo` + workflow filename) and your own
+   protected environment with your own required reviewers — these are not
+   transferable from this repository.
+4. Branch protection, environment protection, and repository secret
+   scanning are repository *settings*, not workflow files — cloning or
+   forking the repo does **not** copy them. They must be re-applied via
+   the GitHub UI or API on the new repository.
+5. GitHub secret scanning and push protection are repository settings that
+   don't carry over to a fork either — re-enable both under the new
+   repository's Security settings, not just Dependabot.
+6. GitGuardian runs as a GitHub App installation scoped to this specific
+   repository, not a workflow file — a fork gets no secret-detection
+   coverage from it until the app is installed separately on the new repo.
+7. CodeQL's `upload-sarif` step in `codeql.yml` only runs meaningfully if
+   Default Setup is *not* already enabled for the repository (it's designed
+   to skip gracefully otherwise) — check whether Default Setup or Advanced
+   Setup is active on the new repository and adjust expectations for where
+   CodeQL findings show up accordingly.
+
 ## Dependency Security Policy
 
 ### Regular Updates