Below is a practical, production-grade architecture for building a **vulnerable binaries database**. I’m going to be explicit about what “such a database” can mean, because there are two materially different products:

1. **Known-build catalog**: “These exact shipped binaries (Build-ID / hash) are affected or fixed for CVE X.”
2. **Binary fingerprint DB**: “Even if the binary is unpackaged / self-built, we can match vulnerable code patterns.”

You want both. The first gets you breadth fast; the second is the moat.

---

## 1) Core principle: treat “binary identity” as the primary key

For Linux ELF:

* Primary: `ELF Build-ID` (from `.note.gnu.build-id`)
* Fallback: `sha256(file_bytes)`
* Add: `sha256(.text)` and/or BLAKE3 for speed

This creates a stable identity that survives “package metadata lies.”

**BinaryKey = build_id || file_sha256**

---

## 2) High-level system diagram

```
            ┌──────────────────────────┐
            │ Vulnerability Intel      │
            │ OSV/NVD + distro advis.  │
            └───────────┬──────────────┘
                        │ normalize
                        v
            ┌──────────────────────────┐
            │ Vuln Knowledge Store     │
            │ CVE↔pkg ranges, patches  │
            └───────────┬──────────────┘
                        │
                        │
┌───────────────────────v─────────────────────────┐
│ Repo Snapshotter (per distro/arch/date)          │
│ - mirrors metadata + packages (+ debuginfo)      │
│ - verifies signatures                            │
│ - emits signed snapshot manifest                 │
└───────────┬───────────────────────────┬─────────┘
            │                           │
            │ packages                  │ debuginfo/sources
            v                           v
┌──────────────────────────┐   ┌──────────────────────────┐
│ Package Unpacker          │   │ Source/Buildinfo Mapper   │
│ - extract files           │   │ - pkg→source commit/patch │
└───────────┬──────────────┘   └───────────┬──────────────┘
            │ binaries                      │
            v                               │
┌──────────────────────────┐               │
│ Binary Feature Extractor  │               │
│ - Build-ID, hashes         │               │
│ - dyn deps, symbols        │               │
│ - function boundaries (opt)│               │
└───────────┬──────────────┘               │
            │                               │
            v                               v
┌──────────────────────────────────────────────────┐
│ Vulnerable Binary Classifier                      │
│ Tier A: pkg/version range                         │
│ Tier B: Build-ID→known shipped build              │
│ Tier C: code fingerprints (function/CFG hashes)   │
└───────────┬───────────────────────────┬──────────┘
            │                           │
            v                           v
┌──────────────────────────┐   ┌──────────────────────────┐
│ Vulnerable Binary DB      │   │ Evidence/Attestation DB   │
│ (indexed by BinaryKey)    │   │ (signed proofs, snapshots)│
└───────────┬──────────────┘   └───────────┬──────────────┘
            │ publish signed snapshot       │
            v                               v
        Clients/Scanners             Explainable VEX outputs
```

---

## 3) Data stores you actually need

### A) Relational store (Postgres)

Use this for *indexes and joins*.

Key tables:

**`binary_identity`**

* `binary_key` (build_id or file_sha256) PK
* `build_id` (nullable)
* `file_sha256`, `text_sha256`
* `arch`, `osabi`, `type` (ET_DYN/EXEC), `stripped`
* `first_seen_snapshot`, `last_seen_snapshot`

**`binary_package_map`**

* `binary_key`
* `distro`, `pkg_name`, `pkg_version_release`, `arch`
* `file_path_in_pkg`, `snapshot_id`

**`snapshot_manifest`**

* `snapshot_id`
* `distro`, `arch`, `timestamp`
* `repo_metadata_digests`, `signing_key_id`, `dsse_envelope_ref`

**`cve_package_ranges`**

* `cve_id`, `ecosystem` (deb/rpm/apk), `pkg_name`
* `vulnerable_ranges`, `fixed_ranges`
* `advisory_ref`, `snapshot_id`

**`binary_vuln_assertion`**

* `binary_key`, `cve_id`
* `status` ∈ {affected, not_affected, fixed, unknown}
* `method` ∈ {range_match, buildid_catalog, fingerprint_match}
* `confidence` (0–1)
* `evidence_ref` (points to signed evidence)

### B) Object store (S3/MinIO)

Do not bloat Postgres with large blobs.

Store:

* extracted symbol lists, string tables
* function hash maps
* disassembly snippets for matched functions (small)
* DSSE envelopes / attestations
* optional: debug info extracts (or references to where they can be fetched)

### C) Optional search index (OpenSearch/Elastic)

If you want fast “find all binaries exporting `SSL_read`” style queries, index symbols/strings.

---

## 4) Building the database: pipelines

### Pipeline 1: Distro repo snapshots → Known-build catalog (breadth)

This is your fastest route to a “binaries DB.”

**Step 1 — Snapshot**

* Mirror repo metadata + packages for (distro, release, arch).
* Verify signatures (APT Release.gpg, RPM signatures, APK signatures).
* Emit **signed snapshot manifest** (DSSE) listing digests of everything mirrored.

**Step 2 — Extract binaries**
For each package:

* unpack (deb/rpm/apk)
* select ELF files (EXEC + shared libs)
* compute Build-ID, file hash, `.text` hash
* store identity + `binary_package_map`

**Step 3 — Assign CVE status (Tier A + Tier B)**

* Ingest distro advisories and/or OSV mappings into `cve_package_ranges`
* For each `binary_package_map`, apply range checks
* Create `binary_vuln_assertion` entries:

  * `method=range_match` (coarse)
* If you have a Build-ID mapping to exact shipped builds, you can tag:

  * `method=buildid_catalog` (stronger than pure version)

This yields a database where a scanner can do:

* “Given Build-ID, tell me all CVEs per the distro snapshot.”

This already reduces noise because the primary key is the **binary**.

---

### Pipeline 2: Patch-aware classification (backports handled)

To handle “version says vulnerable but backport fixed” you must incorporate patch provenance.

**Step 1 — Build provenance mapping**
Per ecosystem:

* Debian/Ubuntu: parse `Sources`, changelogs, (ideally) `.buildinfo`, patch series.
* RPM distros: SRPM + changelog + patch list.
* Alpine: APKBUILD + patches.

**Step 2 — CVE ↔ patch linkage**
From advisories and patch metadata, store:

* “CVE fixed by patch set P in build B of pkg V-R”

**Step 3 — Apply to binaries**
Instead of version-only, decide:

* if the **specific build** includes the patch
* mark as `fixed` even if upstream version looks vulnerable

This is still not “binary-only,” but it’s much closer to truth for distros.

---

### Pipeline 3: Binary fingerprint factory (the moat)

This is where you become independent of packaging claims.

You build fingerprints at the **function/CFG level** for high-impact CVEs.

#### 3.1 Select targets

You cannot fingerprint everything. Start with:

* top shared libs (openssl, glibc, zlib, expat, libxml2, curl, sqlite, ncurses, etc.)
* CVEs that are exploited in the wild / high-severity
* CVEs where distros backport heavily (version logic is unreliable)

#### 3.2 Identify “changed functions” from the fix

Input: upstream commit/patch or distro patch.

Process:

* diff the patch
* extract affected files + functions (tree-sitter/ctags + diff hunks)
* list candidate functions and key basic blocks

#### 3.3 Build vulnerable + fixed reference binaries

For each (arch, toolchain profile):

* compile “known vulnerable” and “known fixed”
* ensure reproducibility: record compiler version, flags, link mode
* store provenance (DSSE) for these reference builds

#### 3.4 Extract robust fingerprints

Avoid raw byte signatures (they break across compilers).

Better fingerprint types, from weakest to strongest:

* **symbol-level**: function name + versioned symbol + library SONAME
* **function normalized hash**:

  * disassemble function
  * normalize:

    * strip addresses/relocs
    * bucket registers
    * normalize immediates (where safe)
  * hash instruction sequence or basic-block sequence
* **basic-block multiset hash**:

  * build a set/multiset of block hashes; order-independent
* **lightweight CFG hash**:

  * nodes: block hashes
  * edges: control flow
  * hash canonical representation

Store fingerprints like:

**`vuln_fingerprint`**

* `cve_id`
* `component` (openssl/libssl)
* `arch`
* `fp_type` (func_norm_hash, bb_multiset, cfg_hash)
* `fp_value`
* `function_hint` (name if present; else pattern)
* `confidence`, `notes`
* `evidence_ref` (points to reference builds + patch)

#### 3.5 Validate fingerprints at scale

This is non-negotiable.

Validation loop:

* Test against:

  * known vulnerable builds (must match)
  * known fixed builds (must not match)
  * large “benign corpus” (estimate false positives)
* Maintain:

  * precision/recall metrics per fingerprint
  * confidence score

Only promote fingerprints to “production” when validation passes thresholds.

---

## 5) Query-time logic (how scanners use the DB)

Given a target binary, the scanner computes:

* `binary_key`
* basic features (arch, SONAME, symbols)
* optional function hashes (for targeted libs)

Then it queries in this precedence order:

1. **Exact match**: `binary_key` exists with explicit assertion (strong)
2. **Build catalog**: Build-ID→known distro build→CVE mapping (strong)
3. **Fingerprint match**: function/CFG hashes hit (strong, binary-only)
4. **Fallback**: package range matching (weakest)

Return result as a signed VEX with evidence references.

---

## 6) Update model: “sealed knowledge snapshots”

To make this auditable and customer-friendly:

* Every repo snapshot is immutable and signed.
* Every fingerprint bundle is versioned and signed.
* Every “vulnerable binaries DB release” is a signed manifest pointing to:

  * which repo snapshots were used
  * which advisory snapshots were used
  * which fingerprint sets were included

This lets you prove:

* what you knew
* when you knew it
* exactly which data drove the verdict

---

## 7) Scaling and cost control

Without control, fingerprinting explodes. Use these constraints:

* Only disassemble/hash functions for:

  * libraries in your “hot set”
  * binaries whose package indicates relevance to a targeted CVE family
* Deduplicate aggressively:

  * identical `.text_sha256` ⇒ reuse extracted functions
  * identical Build-ID across paths ⇒ reuse features
* Incremental snapshots:

  * process only new/changed packages per snapshot
  * store “already processed digest” cache (Valkey)

---

## 8) Security and trust boundaries

A vulnerable binary DB is itself a high-value target. Hardening must be part of architecture:

* Verify upstream repo signatures before ingestion.
* Run unpacking/extraction in sandboxes (namespaces/seccomp) because packages can be hostile.
* Sign:

  * snapshot manifests
  * fingerprint sets
  * DB releases
* Keep signing keys in an HSM/KMS.
* Maintain provenance chain: input digests → output digests.

---

## 9) Minimal viable build plan (no wishful thinking)

### MVP 1: Known-build binary catalog (fast, broad)

* Repo snapshot + Build-ID extraction
* CVE ranges + advisory snapshots
* `binary_key → (pkg@ver, CVEs)` mapping
* Signed snapshot releases

### MVP 2: Patch-aware backport handling (precision jump)

* Source/patch mapping
* Build-specific “fixed-by-backport” logic

### MVP 3: Fingerprints for top components (moat)

* Fingerprint factory for ~20–50 “most reused” libs
* Validation corpus + confidence scoring

---

## 10) What you can claim (and what you should not)

You can defensibly claim:

* “We can identify vulnerable **binaries** (not just packages) with verifiable evidence.”

You should not claim (until you have it):

* “We can detect every vulnerable binary on earth”
  No one can do that without unacceptable false positives/negatives.

---

If you want this aligned tightly to your Stella Ops services split (scanner webservice lattice algorithms + proof-of-integrity graph), I can map the above into:

* concrete microservices,
* queue/job boundaries,
* and the exact API surfaces (`/snapshots`, `/features`, `/fingerprints`, `/match`, `/vex`).
To code **MVP 2 (patch-aware backport handling)** without any human triage, you need one thing in your database that most scanners do not maintain:

> A normalized, distro-specific index:
> **(distro, release, source-package, CVE) → fixed-in distro version (or not-affected / wontfix / unknown), with evidence and confidence.**

Then every scan decision becomes a deterministic version comparison against that index, not against upstream semver.

Below is a concrete, buildable approach (pipelines + data model + code skeletons) that stays fully automated.

---

## 1) What MVP2 computes

### Output table you must build

**`cve_fix_index`**

* `distro` (e.g., debian, ubuntu, rhel, alpine)
* `release` (e.g., bookworm, jammy, 9, 3.19)
* `source_pkg` (not binary subpackage)
* `cve_id`
* `state` ∈ {`fixed`, `vulnerable`, `not_affected`, `wontfix`, `unknown`}
* `fixed_version` (nullable; distro version string, including revision)
* `method` ∈ {`security_feed`, `changelog`, `patch_header`, `upstream_patch_match`}
* `confidence` (float)
* `evidence` (JSON: references to advisory entry, changelog lines, patch names + digests)
* `snapshot_id` (your sealed snapshot identifier)

### Why “source package”?

Security trackers and patch sets are tracked at the **source** level (e.g., `openssl`), while runtime installs are often **binary subpackages** (e.g., `libssl3`). You need a stable join:
`binary_pkg -> source_pkg`.

---

## 2) No-human signals, in strict priority order

You can do this with **zero manual** work by using a tiered resolver:

### Tier 1 — Structured distro security feed (highest precision)

This is the authoritative “backport-aware” answer because it encodes:

* “fixed in 1.1.1n-0ubuntu2.4” (even if upstream says “fixed in 1.1.1o”)
* “not affected” cases
* sometimes arch-specific applicability

Your ingestor just parses and normalizes it.

### Tier 2 — Source package changelog CVE mentions

If a feed entry is missing/late, parse source changelog:

* Debian/Ubuntu: `debian/changelog`
* RPM: `%changelog` in `.spec`
* Alpine: `secfixes` in `APKBUILD` (often present)

This is surprisingly effective because maintainers often include “CVE-XXXX-YYYY” in the entry that introduced the fix.

### Tier 3 — Patch metadata (DEP-3 headers / patch filenames)

Parse patches shipped with the source package:

* Debian: `debian/patches/*` + `debian/patches/series`
* RPM: patch files listed in spec / SRPM
* Alpine: `patches/*.patch` in the aport

Search patch headers and filenames for CVE IDs, store patch hashes.

### Tier 4 — Upstream patch equivalence (optional in MVP2, strong)

If you can map CVE→upstream fix commit (OSV often helps), you can match canonicalized patch hunks against distro patches.

MVP2 can ship without Tier 4; Tier 1+2 already eliminates most backport false positives.

---

## 3) Architecture: the “Fix Index Builder” job

### Inputs

* Your sealed repo snapshot: Packages + Sources (or SRPM/aports)
* Distro security feed snapshot (OVAL/JSON/errata tracker) for same release
* (Optional) OSV/NVD upstream ranges for fallback only

### Processing graph

1. **Build `binary_pkg → source_pkg` map** from repo metadata
2. **Ingest security feed** → produce `FixRecord(method=security_feed, confidence=0.95)`
3. **For source packages in snapshot**:

   * unpack source
   * parse changelog for CVE mentions → `FixRecord(method=changelog, confidence=0.75–0.85)`
   * parse patch headers → `FixRecord(method=patch_header, confidence=0.80–0.90)`
4. **Merge** records into a single best record per key (distro, release, source_pkg, cve)
5. Store into `cve_fix_index` with evidence
6. Sign the resulting snapshot manifest

---

## 4) Merge logic (no human, deterministic)

You need a deterministic rule for conflicts.

Recommended (conservative but still precision-improving):

1. If any record says `not_affected` with confidence ≥ 0.9 → choose `not_affected`
2. Else if any record says `fixed` with confidence ≥ 0.9 → choose `fixed` and `fixed_version = max_fixed_version_among_high_conf`
3. Else if any record says `fixed` at all → choose `fixed` with best available `fixed_version`
4. Else if any says `wontfix` → choose `wontfix`
5. Else `unknown`

Additionally:

* Keep *all* evidence records in `evidence` so you can explain and audit.

---

## 5) Version comparison: do not reinvent it

Backport handling lives or dies on correct version ordering.

### Practical approach (recommended for ingestion + server-side decisioning)

Use official tooling in containerized workers:

* Debian/Ubuntu: `dpkg --compare-versions`
* RPM distros: `rpmdev-vercmp` or `rpm` library
* Alpine: `apk version -t`

This is reliable and avoids subtle comparator bugs.

If you must do it in-process, use well-tested libraries per ecosystem (but containerized official tools are the most robust).

---

## 6) Concrete code: Debian/Ubuntu changelog + patch parsing

This example shows **Tier 2 + Tier 3** inference for a single unpacked source tree. You would wrap this inside your snapshot processing loop.

### 6.1 CVE extractor

```python
import re
from pathlib import Path
from hashlib import sha256

CVE_RE = re.compile(r"\bCVE-\d{4}-\d{4,7}\b")

def extract_cves(text: str) -> set[str]:
    return set(CVE_RE.findall(text or ""))
```

### 6.2 Parse the *top* debian/changelog entry (for this version)

This works well because when you unpack a `.dsc` for version `V`, the top entry is for `V`.

```python
def parse_debian_changelog_top_entry(src_dir: Path) -> tuple[str, set[str], dict]:
    """
    Returns:
      version: str
      cves: set[str] found in the top entry
      evidence: dict with excerpt for explainability
    """
    changelog_path = src_dir / "debian" / "changelog"
    if not changelog_path.exists():
        return "", set(), {}

    lines = changelog_path.read_text(errors="replace").splitlines()
    if not lines:
        return "", set(), {}

    # First line: "pkgname (version) distro; urgency=..."
    m = re.match(r"^[^\s]+\s+\(([^)]+)\)\s+", lines[0])
    version = m.group(1) if m else ""

    entry_lines = [lines[0]]
    # Collect until maintainer trailer line: " -- Name <email>  date"
    for line in lines[1:]:
        entry_lines.append(line)
        if line.startswith(" -- "):
            break

    entry_text = "\n".join(entry_lines)
    cves = extract_cves(entry_text)

    evidence = {
        "file": "debian/changelog",
        "version": version,
        "excerpt": entry_text[:2000],  # store small excerpt, not whole file
    }
    return version, cves, evidence
```

### 6.3 Parse CVEs from patch headers (DEP-3-ish)

```python
def parse_debian_patches_for_cves(src_dir: Path) -> tuple[dict[str, list[dict]], dict]:
    """
    Returns:
      cve_to_patches: {CVE: [ {path, sha256, header_excerpt}, ... ]}
      evidence_summary: dict
    """
    patches_dir = src_dir / "debian" / "patches"
    if not patches_dir.exists():
        return {}, {}

    cve_to_patches: dict[str, list[dict]] = {}

    for patch in patches_dir.glob("*"):
        if not patch.is_file():
            continue
        # Read only first N lines to keep it cheap
        header = "\n".join(patch.read_text(errors="replace").splitlines()[:80])
        cves = extract_cves(header + "\n" + patch.name)
        if not cves:
            continue

        digest = sha256(patch.read_bytes()).hexdigest()
        rec = {
            "path": str(patch.relative_to(src_dir)),
            "sha256": digest,
            "header_excerpt": header[:1200],
        }
        for cve in cves:
            cve_to_patches.setdefault(cve, []).append(rec)

    evidence = {
        "dir": "debian/patches",
        "matched_cves": len(cve_to_patches),
    }
    return cve_to_patches, evidence
```

### 6.4 Produce FixRecords from the source tree

```python
def infer_fix_records_from_debian_source(src_dir: Path, distro: str, release: str, source_pkg: str, snapshot_id: str):
    version, changelog_cves, changelog_ev = parse_debian_changelog_top_entry(src_dir)
    cve_to_patches, patch_ev = parse_debian_patches_for_cves(src_dir)

    records = []

    # Changelog-based: treat CVE mentioned in top entry as fixed in this version
    for cve in changelog_cves:
        records.append({
            "distro": distro,
            "release": release,
            "source_pkg": source_pkg,
            "cve_id": cve,
            "state": "fixed",
            "fixed_version": version,
            "method": "changelog",
            "confidence": 0.80,
            "evidence": {"changelog": changelog_ev},
            "snapshot_id": snapshot_id,
        })

    # Patch-header-based: treat CVE-tagged patches as fixed in this version
    for cve, patches in cve_to_patches.items():
        records.append({
            "distro": distro,
            "release": release,
            "source_pkg": source_pkg,
            "cve_id": cve,
            "state": "fixed",
            "fixed_version": version,
            "method": "patch_header",
            "confidence": 0.87,
            "evidence": {"patches": patches, "patch_summary": patch_ev},
            "snapshot_id": snapshot_id,
        })

    return records
```

That is the automated “patch-aware” signal generator.

---

## 7) Wiring this into your database build

### 7.1 Store raw evidence and merged result

Two-stage storage is worth it:

1. `cve_fix_evidence` (append-only)
2. `cve_fix_index` (merged best record)

So you can:

* rerun merge rules
* improve confidence scoring
* keep auditability

### 7.2 Merging “fixed_version” for a CVE

When multiple versions mention the same CVE, you usually want the **latest** mentioning version (highest by distro comparator), because repeated mentions often indicate earlier partial fix.

Pseudo:

```python
def choose_fixed_version(existing: str | None, candidate: str, vercmp) -> str:
    if not existing:
        return candidate
    return candidate if vercmp(candidate, existing) > 0 else existing
```

Where `vercmp` calls `dpkg --compare-versions` (Debian) or equivalent for that distro.

---

## 8) Decisioning logic at scan time (what changes with MVP2)

Without MVP2, you likely do:

* upstream range check (false positives for backports)

With MVP2, you do:

1. identify `distro+release` from environment (or image base)
2. map `binary_pkg → source_pkg`
3. query `cve_fix_index(distro, release, source_pkg, cve)`
4. if `state=fixed` and `pkg_version >= fixed_version` → fixed
5. if `state=not_affected` → safe
6. else fallback to upstream ranges

That single substitution removes most backport noise.

---

## 9) Practical notes so you don’t get trapped

### A) You must know the distro release

Backport reality is release-specific. The same package name/version can have different patching across releases.

### B) Arch-specific fixes exist

Your schema should allow `arch` on fix records (nullable). If the feed says “only amd64 affected,” store it.

### C) False positives in changelog parsing

Mitigation without humans:

* require CVE mention + security-ish verbs (“fix”, “security”, “patch”) OR presence in patch headers
* otherwise lower confidence and let feed override

### D) Keep evidence small

Store:

* excerpt + patch hashes
  Not entire source tarballs.

---

## 10) Minimal “done definition” for MVP2

You have MVP2 when, for Debian/Ubuntu at least, you can demonstrate:

* A CVE that upstream marks vulnerable for version X
* The distro backported it in X-<revision>
* Your system classifies:

  * `X-older_revision` as vulnerable
  * `X-newer_revision` as fixed
* With evidence: fix feed record and/or changelog/patch proof

No human required.

---

If you want, I can provide the same “Tier 2/3 inference” module for RPM (SRPM/spec parsing) and Alpine (APKBUILD `secfixes` extraction), plus the exact Postgres DDL for `cve_fix_evidence` and `cve_fix_index`, and the merge SQL.