penthera 1.6.1 → 1.7.0

package/docs/METHODOLOGY.md

@@ -1,13 +1,50 @@
 # Methodology
 
-This document describes what Penthera tests, how it decides that something is a
-finding, how sure it is, and where its limits are. Each design choice points to
-the research or standard it rests on. Citation keys such as `[bau2010state]`
-refer to [references.md](references.md) and [references.bib](references.bib).
-
-Measured accuracy on the bundled benchmark is in
-[bench/RESULTS.md](../bench/RESULTS.md); the method behind those numbers is in
-[bench/README.md](../bench/README.md).
+## Abstract
+
+Penthera is an open-source, offline security scanner for web applications,
+their dependencies, and the AI tooling used to build them. This document
+specifies its method. It states the threat model, separates what black-box
+(HTTP) and white-box (repository) analysis can and cannot observe, and defines
+a four-level confidence model that distinguishes deterministic evidence from
+heuristic signals. It describes the false-positive controls built into each
+probe (randomized canaries, context-aware payload selection, baseline
+comparison, and repeated timing measurement) and the non-destructive defaults
+that follow from fail-safe design. Detection rules are distributed only in
+reviewed, versioned releases, never through a live feed, which removes an
+update channel from the attack surface. Each design choice is tied to prior
+research or a published standard. On a bundled benchmark of labelled local
+targets, Penthera reaches a precision of 0.86 and a recall of 0.90. Because the
+same authors wrote the scanner and the targets, these figures measure
+regressions, not accuracy on arbitrary applications.
+
+## How to cite
+
+If you use Penthera or this methodology in research or a report, cite the
+software. The metadata are in [CITATION.cff](../CITATION.cff), which GitHub
+renders as "Cite this repository".
+
+```text
+van der Zwaag, D. (2026). Penthera: An offline security scanner for web apps and AI-built code (Version 1.7.0) [Computer software]. https://github.com/danoszz/penthera
+```
+
+```bibtex
+@software{vanderzwaag2026penthera,
+  author  = {van der Zwaag, Daan},
+  title   = {Penthera: An Offline Security Scanner for Web Apps and {AI}-Built Code},
+  year    = {2026},
+  version = {1.7.0},
+  license = {MIT},
+  url     = {https://github.com/danoszz/penthera}
+}
+```
+
+Citations in this document follow APA 7th edition. Each one resolves to an
+entry in [references.md](references.md), generated from
+[references.bib](references.bib); a test fails if a citation has no entry or an
+entry is never cited. Measured accuracy is in
+[bench/RESULTS.md](../bench/RESULTS.md), and the method behind those numbers is
+in [bench/README.md](../bench/README.md).
 
 ## Contents
 
@@ -23,52 +60,56 @@ Measured accuracy on the bundled benchmark is in
 
 ## Threat model
 
-Penthera is built for small teams shipping web apps and APIs, often with AI
-coding tools, who need a first line of evidence before a human review or a
-paid penetration test. The threat model follows the structure in Shostack
-[shostack2014threat]: what are we building, what can go wrong, what do we do
-about it, and did we do a good job.
+Penthera is built for small teams that ship web apps and APIs, often with AI
+coding tools, and need a first line of evidence before a human review or a paid
+penetration test. The threat model follows the four questions of Shostack
+(2014): what are we building, what can go wrong, what are we going to do about
+it, and did we do a good job.
 
-**Assets.** User data behind the API, credentials and API keys (including AI
-provider keys), the session and identity layer, and the integrity of the code
-and dependencies that get deployed.
+**Assets.** User data behind the API; credentials and API keys, including AI
+provider keys; the session and identity layer; and the integrity of the code and
+dependencies that get deployed.
 
 **Adversaries in scope.**
 
 1. A remote, unauthenticated attacker on the internet who can send arbitrary
-   HTTP requests to the deployed app. This is what the black-box scan models.
-2. An authenticated user trying to reach another user's data (broken object
-   level authorization, the top item in the OWASP API Security Top 10
-   [owasp2023api]). Penthera tests this when given credentials.
+   HTTP requests to the deployed app. The black-box scan models this attacker.
+2. An authenticated user who tries to reach another user's data. Broken object
+   level authorization is the first item in the OWASP API Security Top 10
+   (OWASP Foundation, 2023). Penthera tests for it when given credentials.
 3. Anyone who obtains a copy of the source: a leaked repository, a public fork,
-   a compromised CI log. Meli et al. found secrets leaked in over 100,000
-   public GitHub repositories, with thousands of new, unique secrets leaked
-   every day [meli2019bad]. This is what the
-   white-box secret scan models.
-4. A supply-chain attacker who publishes or compromises a dependency
-   [ladisa2023sok, ohm2020backstabber, zimmermann2019small], including
-   packages that code-generating models invent and attackers then register
-   [spracklen2025package].
-
-**Out of scope.** Physical access, insider threats with production access,
-denial of service, social engineering, and anything that needs exploitation
-beyond a single benign probe. Penthera does not try to replace a human tester;
-it tries to find the issues a scanner can find reliably and say clearly which
-ones it cannot judge.
+   or a compromised CI log. Meli et al. (2019) found secrets leaked in over
+   100,000 public GitHub repositories, with thousands of new, unique secrets
+   leaked every day. The white-box secret scan models this adversary.
+4. A supply-chain attacker who publishes or compromises a dependency (Ladisa et
+   al., 2023; Ohm et al., 2020; Zimmermann et al., 2019), including packages
+   that code-generating models invent and attackers then register (Spracklen
+   et al., 2025).
+
+**Out of scope.** Physical access, insiders with production access, denial of
+service, social engineering, and anything that needs exploitation beyond a
+single benign probe. Penthera does not try to replace a human tester. It tries
+to find the issues a scanner can find reliably, and to say clearly which ones
+it cannot judge.
 
 **Penthera itself is in the threat model.** A security tool runs with the
 user's credentials and network position, so a compromised scanner is a
-compromised machine. Thompson's point that you cannot trust code you did not
-build yourself [thompson1984reflections] applies to scanners and their rule
-feeds. This is why Penthera fetches no rules at run time
+compromised machine. Thompson (1984) showed that you cannot fully trust code you
+did not build yourself; the argument applies to scanners and their rule feeds.
+This is why Penthera fetches no rules at run time
 ([below](#how-new-attack-techniques-are-adopted)).
 
-STRIDE, the threat categories that Shostack's book builds on, originates at
-Microsoft [kohnfelder1999threats]. Penthera's probes map onto it roughly as:
-spoofing (auth, JWT, OAuth, email SPF/DMARC), tampering (injection, CORS),
-repudiation (not tested), information disclosure (exposed files, secrets,
-verbose errors), denial of service (not tested, only rate limiting is
-checked), and elevation of privilege (IDOR/BOLA, client-side-only auth).
+STRIDE, the threat taxonomy that Shostack's book builds on, originates at
+Microsoft (Kohnfelder & Garg, 1999). Penthera's probes map onto it as follows:
+
+| STRIDE category | Penthera coverage |
+|---|---|
+| Spoofing | Authentication, JWT, OAuth, email SPF and DMARC |
+| Tampering | Injection, CORS |
+| Repudiation | Not tested |
+| Information disclosure | Exposed files, secrets, verbose errors |
+| Denial of service | Not tested; only rate limiting is checked |
+| Elevation of privilege | IDOR/BOLA, client-side-only authorization |
 
 ## Black-box and white-box: what each can find
 
@@ -77,40 +118,39 @@ Penthera runs two kinds of analysis and reports them together.
 ### Black-box (URL scan)
 
 The scanner sees only HTTP responses. Its tests are those of the OWASP Web
-Security Testing Guide [owaspwstg42]; each probe's WSTG IDs are listed in
-[owasp-wstg-coverage.md](owasp-wstg-coverage.md).
+Security Testing Guide (OWASP Foundation, n.d.-b); each probe's WSTG IDs are
+listed in [owasp-wstg-coverage.md](owasp-wstg-coverage.md).
 
-What black-box testing finds well: properties that are visible in every
+Black-box testing finds three kinds of issue well: properties visible in every
 response (missing security headers, TLS configuration, cookie flags, CORS
 policy), files and interfaces that should not be public, and injection flaws
-whose effect shows up in the response or its timing. Protocol checks follow
-the relevant specifications: HSTS [hodges2012rfc6797], JWT
-[jones2015rfc7519, sheffer2020rfc8725], and OAuth redirect and PKCE handling
-[lodderstedt2025rfc9700, sakimura2015rfc7636, fett2016comprehensive].
-
-What it misses, and why. Two classic evaluations of black-box scanners point
-the same way. Bau et al. tested eight commercial scanners against a custom
-vulnerable application and older versions of real ones. As a group the tools
-did reasonably well, but second-order flaws, stored XSS and stored SQL
-injection, were missed by many of them [bau2010state]. Doupé et al. tested
-eleven commercial and open-source scanners against WackoPicko, a realistic
-purpose-built app with sixteen planted flaws. Eight of the sixteen were missed
-by every scanner, including stored SQL injection, multi-step stored XSS,
-forceful browsing and a business logic flaw. They concluded that crawling
-matters as much as detection: a scanner cannot test a page it never reaches,
-and losing track of state (logins, multi-step forms) is a main reason it
-doesn't [doupe2010johnny].
+whose effect shows in the response or its timing. Protocol checks follow the
+relevant specifications: HSTS (Hodges et al., 2012), JWT (Jones et al., 2015;
+Sheffer et al., 2020), and OAuth redirect and PKCE handling (Fett et al., 2016;
+Lodderstedt et al., 2025; Sakimura et al., 2015).
+
+Two classic evaluations of black-box scanners show what this approach misses.
+Bau et al. (2010) tested eight commercial scanners against a custom vulnerable
+application and older versions of real ones. As a group the tools did
+reasonably well, but many of them missed second-order flaws such as stored XSS
+and stored SQL injection. Doupé et al. (2010) tested eleven commercial and
+open-source scanners against WackoPicko, a realistic purpose-built app with
+sixteen planted flaws. Every scanner missed eight of the sixteen, among them
+stored SQL injection, multi-step stored XSS, forceful browsing, and a business
+logic flaw. They concluded that crawling matters as much as detection: a
+scanner cannot test a page it never reaches, and losing track of state (logins,
+multi-step forms) is a main reason it does not reach it.
 
 Penthera's design responds to each point:
 
 - **Crawl coverage.** Endpoint discovery uses a wordlist plus the app's own
   OpenAPI document when one is exposed, and records exactly which probes ran.
-  The WSTG coverage table in every report lists tests as run or not run, so a
-  missing check is never presented as a pass.
+  The WSTG coverage table in every report lists each test as run or not run, so
+  a missing check is never presented as a pass.
 - **State and logic.** Penthera does not claim to find business logic flaws,
-  which no scanner in the Doupé et al. study found either.
-  IDOR/BOLA results are labelled `needs-human-review` because a scanner cannot
-  know whether user A is allowed to read object B.
+  which no scanner in the study by Doupé et al. (2010) found either. IDOR/BOLA
+  results are labelled `needs-human-review` because a scanner cannot know
+  whether user A is allowed to read object B.
 - **Stored and second-order flaws.** Not tested. They need a write followed by
   a read elsewhere, which conflicts with the non-destructive default.
 
@@ -119,33 +159,32 @@ Penthera's design responds to each point:
 The scanner reads source files. It finds hardcoded secrets, route handlers and
 their authentication boundaries, and risky code patterns.
 
-Secret detection uses provider-specific prefixes (for example `AKIA` for AWS,
-`sk-ant-` for Anthropic) plus a small number of assignment patterns such as
-`api_key = "..."` with a placeholder filter. Meli et al. took the same
-conservative route, restricting detection to private keys and API keys with
-distinctive formats [meli2019bad]. The cost is recall: a secret with no
-recognisable format is invisible to this approach. SecretBench, a labelled
-dataset of real secrets across many formats, is the natural yardstick for that
-gap [basak2023secretbench]. The benchmark here includes an unprefixed signing
-key that Penthera misses for this reason.
+Secret detection uses provider-specific prefixes (for example `AKIA` for AWS
+and `sk-ant-` for Anthropic) plus a small number of assignment patterns such as
+`api_key = "..."` with a placeholder filter. Meli et al. (2019) took the same
+conservative route and restricted detection to private keys and API keys with
+distinctive formats. The cost is recall: a secret with no recognisable format
+is invisible to this approach. SecretBench, a labelled dataset of real secrets
+across many formats, is the natural yardstick for that gap (Basak et al.,
+2023). The bundled benchmark includes an unprefixed signing key that Penthera
+misses for this reason.
 
-What white-box scanning cannot see: runtime configuration (headers added by a
-CDN, a WAF in front of the app), secrets injected at deploy time, and anything
-in dependencies that is only known from a vulnerability database.
+White-box scanning cannot see runtime configuration (headers added by a CDN, a
+WAF in front of the app), secrets injected at deploy time, or anything in
+dependencies that is only known from a vulnerability database.
 
 ### Combining them
 
 Running both against the same app catches cases neither sees alone: a route
 the repository marks as public that the black-box scan confirms is reachable,
-or a header the code sets that the edge strips. The report keeps the source of
+or a header the code sets that the edge strips. The report keeps the origin of
 each finding (`source`, `method`) so a reader can tell which side produced it.
 
 ## Confidence model
 
 Severity says how bad a finding would be if real. Confidence says how likely it
-is to be real. Penthera reports both, and never lets a heuristic look like a
-fact. The labels are defined in
-[lib/provenance.js](../lib/provenance.js):
+is to be real. Penthera reports both and never lets a heuristic look like a
+fact. The labels are defined in [lib/provenance.js](../lib/provenance.js):
 
 | Label | Meaning | Typical sources |
 |---|---|---|
@@ -154,120 +193,121 @@ fact. The labels are defined in
 | `potential` | A heuristic or one-shot signal that needs corroboration. | Fuzzer, adaptive probes |
 | `needs-human-review` | Exploitability cannot be judged from outside. | IDOR/BOLA, client-side-only auth |
 
-Every finding also carries `source`, `method` and `collected_at`, and these
-travel into SARIF so the label survives into GitHub code scanning.
+Every finding also carries `source`, `method`, and `collected_at`. These travel
+into SARIF, so the label survives into GitHub code scanning.
 
-The benchmark reports precision per confidence label, which is the check that
-the labels mean what they say. On the current run all `likely` and
-`needs-human-review` findings were true positives, the one `potential` finding
-was a false positive, and the two `confirmed` false positives are cases where
-the evidence is real but the judgement is wrong (a health endpoint that is
-public by design, AWS's published example key). See
+The benchmark reports precision per confidence label, which tests whether the
+labels mean what they say. On the current run, all `likely` and
+`needs-human-review` findings were true positives and the one `potential`
+finding was a false positive. The two `confirmed` false positives are cases
+where the evidence is real but the judgement is wrong: a health endpoint that
+is public by design, and AWS's published example key. See
 [bench/RESULTS.md](../bench/RESULTS.md).
 
 ## False-positive controls
 
-Black-box scanners lose trust through false positives faster than through
-misses. Specific controls in the probes:
+A black-box scanner loses trust through false positives faster than through
+misses. The probes apply these controls:
 
 - **Randomized canaries.** The SSTI probe multiplies two random four-digit
-  numbers and looks for the seven- or eight-digit product, and only when the
-  raw payload and the literal expression are absent from the response
+  numbers and looks for the seven- or eight-digit product, and only when
+  neither the raw payload nor the literal expression appears in the response
   ([lib/injections.js](../lib/injections.js), `buildSstiProbes`). The common
-  fixed `7*7 = 49` canary fires on any page that happens to contain "49". XSS
-  probes use a per-probe random reflection marker (`makeCanary`).
+  fixed canary `7*7 = 49` fires on any page that happens to contain "49". XSS
+  probes use a random reflection marker per probe (`makeCanary`).
 - **Context before payload.** The XSS probe first checks where its marker is
-  reflected (HTML body, attribute, script) and only sends payloads that would
-  execute in that context, then checks they came back unencoded. This is the
-  approach of context-aware tools such as Dalfox.
-- **Baseline comparison.** Error-based SQL injection is only reported when the
+  reflected (HTML body, attribute, or script), sends only payloads that would
+  execute in that context, and then checks that they came back unencoded.
+  Context-aware tools such as Dalfox take the same approach.
+- **Baseline comparison.** Error-based SQL injection is reported only when the
   database error appears in the injected response and not in the baseline.
 - **Timing re-sampling.** A single slow response proves nothing: garbage
-  collection, cold starts and network jitter all look like an injected sleep.
-  Time-based SQL and command injection candidates are re-sent and only
-  reported when the median delay holds (`confirmTimingDelay`). Crosby et al.
+  collection, cold starts, and network jitter all look like an injected sleep.
+  Time-based SQL and command injection candidates are re-sent and reported only
+  when the median delay holds (`confirmTimingDelay`). Crosby et al. (2009)
   showed that network jitter dominates single remote timing measurements and
-  that filtering over many samples is what makes them usable
-  [crosby2009opportunities], building on Kocher's original timing attacks
-  [kocher1996timing]. Penthera's delays are seconds, not microseconds, so a
-  median of three samples is enough.
-- **Host-checked redirects.** An open redirect is reported only if the
-  `Location` header actually resolves to the attacker host, not when the
-  payload merely appears in a same-site redirect's query string.
+  that filtering over many samples is what makes them usable, building on the
+  original timing attacks of Kocher (1996). Penthera's injected delays are
+  seconds, not microseconds, so a median of three samples is enough.
+- **Host-checked redirects.** An open redirect is reported only when the
+  `Location` header resolves to the attacker host, not when the payload merely
+  appears in the query string of a same-site redirect.
 - **Context-aware suppression.** On localhost and private hosts, findings that
-  do not apply (no HTTPS, missing `Secure` on cookies) are suppressed.
+  do not apply there (no HTTPS, missing `Secure` on cookies) are suppressed.
 
-The benchmark's decoy target exercises each of these with an endpoint built to
-fool a naive scanner. Writing it found one real problem in the decoy itself: a
+The benchmark's decoy target exercises each control with an endpoint built to
+fool a naive scanner. Writing it exposed one real flaw in the decoy itself: a
 "safe" redirect that accepted `/\evil.com`, which browsers treat as
 `//evil.com`. Penthera reported it correctly.
 
 ## Non-destructive by default
 
 The `quick` and `standard` profiles send only requests a normal browser or API
-client would send: GETs, `OPTIONS`, and invalid login attempts. They do not
+client would send: `GET`, `OPTIONS`, and invalid login attempts. They do not
 send attack payloads, create or modify data, or exploit anything they find.
 
 Payload-based testing (`--deep`, `--fuzz`, `--adaptive`, or `--profile deep`)
-is opt-in and gated behind a confirmation prompt. Even then each probe sends a
-benign marker (a random string, arithmetic, a short sleep, `id`) rather than a
-working exploit, and stops at the first confirmation per endpoint. The
-adaptive engine may send unexpected HTTP methods, including `DELETE`, to
-routes with placeholder IDs; it is therefore never part of a default run.
-
-This follows Saltzer and Schroeder's fail-safe defaults and least privilege
-[saltzer1975protection]: the default does the least that is still useful, and
-anything riskier needs an explicit decision. NIST SP 800-115 makes the same
-distinction between non-intrusive assessment and penetration testing, and
-recommends written rules of engagement before the latter
-[scarfone2008sp800115].
+is opt-in and gated behind a confirmation prompt. Even then, each probe sends a
+benign marker (a random string, an arithmetic expression, a short sleep, `id`)
+rather than a working exploit, and stops at the first confirmation per
+endpoint. The adaptive engine may send unexpected HTTP methods, including
+`DELETE`, to routes with placeholder IDs, so it is never part of a default run.
+
+This follows the principles of fail-safe defaults and least privilege set out by
+Saltzer and Schroeder (1975): the default does the least that is still useful,
+and anything riskier needs an explicit decision. NIST SP 800-115 draws the same
+line between non-intrusive assessment and penetration testing, and recommends
+written rules of engagement before the latter (Scarfone et al., 2008).
 
 ## Offline and no telemetry
 
-Penthera does not phone home. It sends no usage data, analytics or crash
+Penthera does not phone home. It sends no usage data, analytics, or crash
 reports, and it has no accounts. Reports are written to local files.
 
 Network traffic goes to the target you name, with two documented exceptions:
 
-1. `--recon` (and the `deep` profile) queries public OSINT sources (crt.sh,
-   the Wayback Machine, AlienVault OTX) with the target domain. It is skipped
-   for localhost.
+1. `--recon` (and the `deep` profile) queries public OSINT sources (crt.sh, the
+   Wayback Machine, AlienVault OTX) with the target domain. It is skipped for
+   localhost.
 2. The Retire.js check downloads the public Retire.js vulnerability database
-   from GitHub to compare JavaScript library versions locally. This is data,
-   not code: it is parsed as JSON and never executed. It is the one place a
-   detection input arrives at run time, and the roadmap's `--offline` egress
-   guard replaces it with a vendored copy shipped in releases.
-
-The benchmark enforces offline operation mechanically: it wraps `fetch` so any
-request to a non-loopback host is refused and counted, and fails if the count
-is not zero.
-
-These choices follow economy of mechanism and complete mediation
-[saltzer1975protection]: fewer network paths means fewer things to audit, and
-a tool that talks only to the target is easy to reason about in a regulated
-environment.
+   from GitHub and compares JavaScript library versions locally. Outdated
+   client-side libraries are common on the web and often carry known
+   vulnerabilities (Lauinger et al., 2017). The database is data, not code: it
+   is parsed as JSON and never executed. It is the one place a detection input
+   arrives at run time. Under `--offline`, and whenever the download fails,
+   Penthera uses the snapshot vendored in the release instead.
+
+The benchmark enforces offline operation mechanically. It wraps `fetch` so any
+request to a non-loopback host is refused and counted, and it fails if the
+count is not zero.
+
+These choices follow the principles of economy of mechanism and complete
+mediation (Saltzer & Schroeder, 1975): fewer network paths mean fewer things to
+audit, and a tool that talks only to its target is easy to reason about in a
+regulated environment.
 
 ## How new attack techniques are adopted
 
-Attack techniques change quickly. In the last few years: indirect prompt
-injection against LLM-integrated apps [greshake2023signed, perez2022ignore,
-liu2023prompt], package hallucination and slopsquatting
-[spracklen2025package], and attacks on agent tooling and MCP servers
-catalogued by OWASP [owasp2024llmtop10, owasp2025agentic, owasp2025mcptop10]
-and MITRE ATLAS [mitreatlas]. A scanner that does not keep up becomes a
-false sense of security.
+Attack techniques change quickly. Recent examples include indirect prompt
+injection against LLM-integrated applications (Greshake et al., 2023; Liu et
+al., 2023; Perez & Ribeiro, 2022), package hallucination and slopsquatting
+(Spracklen et al., 2025), and attacks on agent tooling and MCP servers,
+catalogued by OWASP (OWASP Foundation, 2024, 2025a, 2025b) and in MITRE ATLAS
+(The MITRE Corporation, n.d.-b). A scanner that does not keep up gives a false
+sense of security.
 
-Penthera keeps up through reviewed releases, not through live updates:
+Penthera keeps up through reviewed releases, not live updates:
 
-- **Rules ship as code in a release.** New probes, patterns and templates are
+- **Rules ship as code in a release.** New probes, patterns, and templates are
   added by pull request, reviewed, tested against the benchmark, and published
   in a versioned release with a CHANGELOG entry. There is no rule server, no
   background update, and no command that fetches rules from the internet.
 - **Every new rule carries a source and a date.** A rule added after v1.2.0
   records where the technique comes from (a paper, an advisory, an OWASP or
-  ATLAS entry, an incident write-up) and the date it was added. Categories are
-  already linked to their sources in [lib/references.json](../lib/references.json);
-  the built-in rules that predate this policy are being backfilled.
+  ATLAS entry, an incident write-up) and the date it was added. Finding
+  categories are already linked to their sources in
+  [lib/references.json](../lib/references.json); the built-in rules that
+  predate this policy are being backfilled.
 - **Every new rule comes with a benchmark case.** A detection rule is added
   together with a labelled true positive and, where a false positive is
   plausible, a decoy in [bench/](../bench/). The CI floor in the benchmark
@@ -276,25 +316,39 @@ Penthera keeps up through reviewed releases, not through live updates:
   load YAML templates from directories you choose. Penthera does not download
   them.
 
-Why not auto-update? A rule feed is a code path from someone else's server
-into a tool that runs with your network access and often your credentials.
-Supply-chain research shows that update channels and package registries are
-exactly where attackers insert themselves [ladisa2023sok, ohm2020backstabber,
-zimmermann2019small], and that securing an update channel needs signed
-metadata, key rotation and explicit trust delegation [samuel2010survivable,
-torresarias2019intoto]. Shipping rules inside the signed, versioned package
-reuses the trust you already place in the release, and gives a clear audit
-trail: the rules you ran are the rules in the version you installed.
+Why not update automatically? A rule feed is a code path from someone else's
+server into a tool that runs with your network access and often your
+credentials. Supply-chain research shows that update channels and package
+registries are exactly where attackers insert themselves (Ladisa et al., 2023;
+Ohm et al., 2020; Zimmermann et al., 2019), and that securing an update channel
+needs signed metadata, key rotation, and explicit trust delegation (Samuel et
+al., 2010; Torres-Arias et al., 2019). Shipping rules inside the signed,
+versioned package reuses the trust you already place in the release, and gives
+a clear audit trail: the rules you ran are the rules in the version you
+installed.
 
 ## Citations in reports
 
 Each finding category maps to one to three references in
-[lib/references.json](../lib/references.json). They appear:
+[lib/references.json](../lib/references.json), chosen to explain why the
+finding matters. Besides the sources discussed above, these include the
+empirical work behind specific header and policy checks: Content Security
+Policy (Weichselbaum et al., 2016), cookie handling and cross-site request
+forgery (Barth et al., 2008), and CORS misconfiguration
+(Chen et al., 2018). Email authentication findings cite the SPF and DMARC
+specifications (Kitterman, 2014; Kucherawy & Zwicky, 2015). Injection,
+exposure, and configuration findings cite the OWASP Top 10 (OWASP Foundation,
+2021, 2025c), code-pattern findings cite the Common Weakness Enumeration (The
+MITRE Corporation, n.d.-a), and license findings use the identifiers of the
+SPDX License List (SPDX Workgroup, The Linux Foundation, n.d.).
+
+The references appear in two places:
 
 - in the Markdown report, as a "Why this matters / Sources" line under each
   finding and a "Sources" line under each action-plan item;
-- in SARIF [oasis2023sarif], as the rule's `helpUri` (first source) and
-  `help` text (all sources), and as `properties.references` (the BibTeX keys).
+- in SARIF (Fanning & Golding, 2023), as the rule's `helpUri` (first source)
+  and `help` text (all sources), and as `properties.references` (the BibTeX
+  keys).
 
 [references.md](references.md) and the `sources` block of `references.json`
 are generated from [references.bib](references.bib) by
@@ -303,19 +357,19 @@ are generated from [references.bib](references.bib) by
 ## Known limitations
 
 - No authenticated crawling beyond the bearer token or cookie you pass, so
-  pages behind multi-step flows are not reached [doupe2010johnny].
-- No stored or second-order injection testing [bau2010state].
-- No DOM-based XSS analysis; Penthera does not run JavaScript
-  [lekies2013flows, stock2014precise].
-- No business logic testing. IDOR/BOLA findings need a human to confirm.
-- Secret detection is pattern-based and skips Markdown and other
-  documentation files, so unprefixed secrets and secrets in notes are missed.
+  pages behind multi-step flows are not reached (Doupé et al., 2010).
+- No stored or second-order injection testing (Bau et al., 2010).
+- No DOM-based XSS analysis, because Penthera does not run JavaScript (Lekies et
+  al., 2013; Stock et al., 2014).
+- No business logic testing. IDOR/BOLA findings need a human to confirm them.
+- Secret detection is pattern-based and skips Markdown and other documentation
+  files, so unprefixed secrets and secrets in notes are missed.
 - The bundled benchmark was written by the same people as the scanner. Its
   numbers measure regressions and the false-positive controls, not accuracy on
   arbitrary applications. Independent benchmarks such as the OWASP Benchmark
-  [owaspbenchmark] and the approach of Antunes and Vieira
-  [antunes2010benchmarking, antunes2015assessing] are the model for a fairer
-  comparison, and scoring against labelled third-party targets (Juice Shop,
-  crAPI) is the next step.
-- Compliance output (NIS2 [eu2022nis2]) is evidence toward a duty of care, not
-  a certification.
+  (OWASP Foundation, n.d.-a) and the benchmarking approach of Antunes and Vieira
+  (2010, 2015) are the model for a fairer comparison. Scoring against labelled
+  third-party targets (Juice Shop, crAPI) is the next step.
+- Compliance output for the NIS2 Directive (European Parliament and Council of
+  the European Union, 2022) is evidence toward a duty of care, not a
+  certification.

package/docs/commands/README.md

@@ -6,6 +6,7 @@ has the full flag list.
 
 | Command | Page | What it does |
 |---|---|---|
+| `penthera`, `penthera init` | [init.md](init.md) | Set up in one command: detect, check, then hook, workflow and dashboard |
 | `penthera <url>`, `--repo .` | [scan.md](scan.md) | Scan a running app and its source: modes, profiles, outputs, exit codes, CI |
 | `penthera agents` | [agents.md](agents.md) | Audit skills, MCP servers, hooks, plugins and rule files |
 | `penthera deps` | [deps.md](deps.md) | What each package can do, the upgrade diff, typosquats, license policy |
@@ -14,7 +15,7 @@ has the full flag list.
 | `penthera hook` | [hook.md](hook.md) | Pre-commit hook for secrets, agent config and dependency changes |
 | GitHub Action | [action.md](action.md) | The capability diff as a pull-request comment, plus SARIF |
 | Agent Skill | [skill.md](skill.md) | Let Claude Code, Cursor and other agents drive Penthera |
-| `penthera ui` | [dashboard.md](../dashboard.md) | The local dashboard: posture, findings, history, evidence, and the fix loop from the page |
+| `penthera ui` | [dashboard.md](../dashboard.md) | The local dashboard: one view with projects, findings, side cards, and the fix loop from the page |
 
 Compliance flags (`--framework nis2`, `--readiness`, `--cra`, `--aibom`, ...)
 are covered in [compliance-nis2.md](../compliance-nis2.md) and