Merge PR #16: browsable run reports, resume and auth fixes

feat: browse a run's results in the browser, plus resume and auth fixes

.gitignore

@@ -51,3 +51,6 @@ docs/_site/
 .jekyll-cache
 docs/.jekyll-cache/
 _site/
+
+# local research artifacts: run logs, generated reports, scratch previews
+research/

pipelines/loldrivers/pipeline.yaml

@@ -13,7 +13,21 @@ name: loldrivers
 description: windows kernel driver vulnerability research pipeline
 version: "2.0"
 
-model: claude-code/sonnet
+model: claude-code/opus
+
+# how `deepzero report` presents this pipeline's results. every field is
+# optional - a pipeline that declares nothing still gets a useful report.
+report:
+  title: Windows kernel driver review
+  entity: driver
+  classification_key: classification
+  vulnerable_when: [vulnerable]
+  safe_when: [safe]
+  columns:
+    - semgrep_scanner.finding_count
+    - discover.priority_score
+    - decompile.function_count
+    - discover.dangerous_imports
 
 settings:
   work_dir: work

src/deepzero/cli.py

@@ -174,8 +174,10 @@ def run(
     # ensure built-in stages are registered
     import deepzero.stages  # noqa: F401
     from deepzero.engine.pipeline import load_pipeline
+    from deepzero.engine.report import write_report
     from deepzero.engine.state import RunState, StateStore
 
+    log_report = logging.getLogger("deepzero.report")
     target_path = Path(target).resolve()
 
     try:
@@ -246,6 +248,12 @@ def run(
     if is_resume:
         run_state = existing_run
         run_state.status = RunStatus.RUNNING
+        # the pipeline's model may have changed since the run was created; record
+        # what this resumed run will actually call so status/reports don't lie
+        if run_state.model != pipeline_def.model:
+            log_msg = f"model changed since last run: {run_state.model or '(unset)'} -> {pipeline_def.model}"
+            console.print(f"[yellow]![/] {log_msg}")
+            run_state.model = pipeline_def.model
     else:
         # initialize fresh state
         state_store.save_pipeline_snapshot(pipeline_def.raw_yaml)
@@ -257,7 +265,79 @@ def run(
             model=pipeline_def.model,
         )
 
-    run_state = runner.run(target_path, run_state)
+    # a live report the user can open straight away and watch fill in. it is
+    # rebuilt when results actually land rather than on a timer, and rate
+    # limited so a fast stage cannot spend the run's time writing html
+    report_dir = pipeline_def.work_dir / "report"
+    report_index = report_dir / "index.html"
+    last_written = [0.0]
+
+    def _refresh_report(force: bool = False) -> None:
+        if not force and time.monotonic() - last_written[0] < 15:
+            return
+        try:
+            write_report(pipeline_def.work_dir, report_dir, config=pipeline_def.report)
+            last_written[0] = time.monotonic()
+        except (OSError, ValueError, KeyError, TypeError) as exc:
+            log_report.debug("could not refresh the report: %s", exc)
+
+    _refresh_report(force=True)
+    console.print(f" report   [bold]{report_index.resolve().as_uri()}[/]")
+    console.print(" [dim]open it now - it updates itself as results land[/]\n")
+
+    runner.progress_hook = _refresh_report
+    try:
+        run_state = runner.run(target_path, run_state)
+    finally:
+        _refresh_report(force=True)  # settle the final state, no reload banner
+        console.print(f"\n report   [bold]{report_index.resolve().as_uri()}[/]")
+
+
+@main.command()
+@click.option("--pipeline", "-p", default=None, help="pipeline name or path")
+@click.option("--work-dir", "-w", default=None, help="work directory (overrides --pipeline)")
+@click.option("--out", "-o", default=None, help="output directory (default <work_dir>/report)")
+@click.option("--open", "open_browser", is_flag=True, help="open the report when finished")
+@click.option("--verbose", "-v", is_flag=True, help="verbose logging")
+def report(
+    pipeline: str | None, work_dir: str | None, out: str | None, open_browser: bool, verbose: bool
+):
+    """build a browsable HTML report from a run's results (safe mid-run)"""
+    _setup_logging(verbose)
+
+    from deepzero.engine.report import write_report
+
+    report_cfg: dict = {}
+    if work_dir:
+        work_path = Path(work_dir)
+    elif pipeline:
+        import deepzero.stages  # noqa: F401
+        from deepzero.engine.pipeline import load_pipeline
+
+        _load_env()
+        try:
+            pipeline_def = load_pipeline(pipeline)
+        except ValueError as e:
+            console.print(f"[bold red]X ERROR[/]: {e}")
+            raise SystemExit(1)
+        work_path = pipeline_def.work_dir
+        report_cfg = pipeline_def.report
+    else:
+        console.print("[bold red]X ERROR[/]: pass --pipeline or --work-dir")
+        raise SystemExit(1)
+
+    if not work_path.exists():
+        console.print(f"[bold red]X ERROR[/]: work directory does not exist: {work_path}")
+        raise SystemExit(1)
+
+    html_path, json_path = write_report(work_path, Path(out) if out else None, config=report_cfg)
+    console.print(f"[green]\\[ok][/] report written to [bold]{html_path}[/]")
+    console.print(f"      machine-readable copy: {json_path}")
+
+    if open_browser:
+        import webbrowser
+
+        webbrowser.open(html_path.resolve().as_uri())
 
 
 @main.command()

src/deepzero/engine/backends/claude_code.py

@@ -15,10 +15,16 @@ import sys
 from pathlib import Path
 from typing import Any, ClassVar
 
-from deepzero.engine.backends.base import BackendError, CLIAgentBackend
+from deepzero.engine.backends.base import BackendAuthError, BackendError, CLIAgentBackend
 
 log = logging.getLogger("deepzero.llm.claude_code")
 
+# what to tell the user when the cli reports an auth failure. deepzero does not
+# inspect claude's credential store: whatever auth the cli has is the auth we
+# use, and if it has none the cli says so and we relay it.
+_AUTH_HINT = "run `claude` in a terminal and sign in, then retry"
+
+
 # the prompt carries untrusted content (decompiled malware, attacker-controlled
 # strings). a completion never needs tools, so deny the ones that could turn a
 # prompt injection into code execution or exfiltration.
@@ -43,11 +49,8 @@ class ClaudeCodeBackend(CLIAgentBackend):
     binary_names: ClassVar[tuple[str, ...]] = ("claude",)
     install_hint: ClassVar[str] = "install it and sign in (https://claude.com/claude-code)."
     # never use --bare: it disables oauth/keychain reads, which is exactly the
-    # auth this backend exists to use
-    subscription_auth_env_blocklist: ClassVar[tuple[str, ...]] = (
-        "ANTHROPIC_API_KEY",
-        "ANTHROPIC_AUTH_TOKEN",
-    )
+    # auth this backend exists to use. the cli decides how to authenticate from
+    # its own config and environment - deepzero does not second-guess it.
 
     def __init__(self, model: str, **kwargs: Any):
         super().__init__(model, **kwargs)
@@ -71,6 +74,13 @@ class ClaudeCodeBackend(CLIAgentBackend):
             paths.append(home / ".local" / "bin" / "claude.exe")
         return paths
 
+    def classify_error(self, detail: str, status: Any = None) -> BackendError:
+        err = super().classify_error(detail, status)
+        # the cli's own auth message is the source of truth; just add the remedy
+        if isinstance(err, BackendAuthError):
+            return BackendAuthError(f"{err} - {_AUTH_HINT}")
+        return err
+
     def build_argv(self, system: str) -> tuple[list[str], str]:
         argv = [str(self._binary), "-p", "--output-format", "json"]
 

src/deepzero/engine/llm.py

@@ -38,9 +38,9 @@ class LLMProvider:
         """send messages to the llm and return the response text.
         handles rate limiting with adaptive backoff."""
         backend = self.backend
-        # forward all options; each backend uses what applies (litellm passes
-        # generation kwargs to the api, cli backends read controls like timeout
-        # and ignore the rest) so e.g. timeout= is not silently dropped
+        # every option is forwarded and each backend takes what applies to it:
+        # litellm passes generation kwargs to the api, while cli backends read
+        # controls such as timeout and ignore the rest
         merged = {**self.default_kwargs, **kwargs}
         backoff = initial_backoff
 

src/deepzero/engine/pipeline.py

@@ -35,6 +35,7 @@ class PipelineDefinition:
         stage_specs: list[StageSpec],
         pipeline_dir: Path,
         raw_yaml: str,
+        report: dict[str, Any] | None = None,
     ):
         self.name = name
         self.description = description
@@ -44,6 +45,9 @@ class PipelineDefinition:
         self.stage_specs = stage_specs
         self.pipeline_dir = pipeline_dir
         self.raw_yaml = raw_yaml
+        # optional presentation hints for `deepzero report` - pipelines that
+        # declare nothing still get a useful report
+        self.report = report or {}
 
         # resolved processor instances
         self.ingest_processor: IngestProcessor | None = None
@@ -138,6 +142,7 @@ def load_pipeline(
         name=name,
         description=description,
         model=model,
+        report=data.get("report") or {},
         settings=settings,
         knowledge=knowledge,
         stage_specs=stage_specs,

src/deepzero/engine/runner.py

@@ -9,7 +9,7 @@ import threading
 import time
 import traceback as tb_module
 from pathlib import Path
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, Callable
 
 from rich.console import Console
 
@@ -76,6 +76,7 @@ class PipelineRunner:
         default_max_workers: int = 4,
         console: Console | None = None,
         dashboard: PipelineDashboard | None = None,
+        progress_hook: Callable[[], None] | None = None,
     ):
         self.ingest = ingest
         self.stages = stages
@@ -86,9 +87,20 @@ class PipelineRunner:
         self.default_max_workers = default_max_workers
         self.console = console or Console()
         self.dashboard = dashboard
+        # called when new results have landed, so a caller can refresh a live
+        # view. never allowed to interrupt the run
+        self.progress_hook = progress_hook
         self._shutdown_event = threading.Event()
         self._original_sigint = None
 
+    def _notify_progress(self) -> None:
+        if self.progress_hook is None:
+            return
+        try:
+            self.progress_hook()
+        except Exception as exc:  # noqa: BLE001 - a view refresh must never fail a run
+            log.debug("progress hook failed: %s", exc)
+
     def _make_entry(self, state: SampleState) -> ProcessorEntry:
         # centralizes ProcessorEntry construction for map/reduce/batch
         return ProcessorEntry(
@@ -223,6 +235,8 @@ class PipelineRunner:
             else:
                 self._run_map(processor, active, spec, stage_stats)
 
+            self._notify_progress()
+
             self._apply_stage_limit(spec, sample_states, stage_stats)
 
             elapsed = time.monotonic() - t0
@@ -460,6 +474,7 @@ class PipelineRunner:
                     for s in dirty:
                         self.state_store.save_sample(s)
                     dirty.clear()
+                    self._notify_progress()
             for s in dirty:
                 self.state_store.save_sample(s)
         else:
@@ -507,6 +522,7 @@ class PipelineRunner:
                         for s in dirty:
                             self.state_store.save_sample(s)
                         dirty.clear()
+                        self._notify_progress()
             for s in dirty:
                 self.state_store.save_sample(s)
 
@@ -522,7 +538,9 @@ class PipelineRunner:
 
         if result.status == StageStatus.COMPLETED:
             if result.data and "__skipped" in result.data:
-                state.mark_stage_skipped(spec.name, result.data["__skipped"])
+                # work that was already done counts as passed and the sample
+                # continues to the next stage, per MapProcessor.should_skip
+                state.mark_stage_cached(spec.name, result.data["__skipped"])
             else:
                 state.mark_stage_completed(
                     spec.name,

src/deepzero/engine/state.py

@@ -51,6 +51,9 @@ class StageOutput:
     # namespaced processor output - never merged across stages
     data: dict[str, Any] = field(default_factory=dict)
     error: str | None = None
+    # why this stage did no work (cached output, filtered out). kept separate from
+    # error so a normal skip is never reported as a failure
+    skip_reason: str = ""
 
 
 @dataclass
@@ -105,6 +108,22 @@ class SampleState:
         self.error = error
         self.verdict = SampleStatus.FAILED
 
+    def mark_stage_cached(self, stage_name: str, reason: str = "") -> None:
+        """work for this stage was already done (e.g. output already on disk).
+
+        the sample stays in the pipeline: per MapProcessor.should_skip, a skipped
+        sample counts as passed. this is NOT mark_stage_skipped, which filters the
+        sample out of the run entirely.
+        """
+        if stage_name not in self.history:
+            self.history[stage_name] = StageOutput()
+        stage = self.history[stage_name]
+        stage.status = StageStatus.COMPLETED
+        stage.verdict = Verdict.CONTINUE
+        stage.completed_at = _now()
+        if reason:
+            stage.skip_reason = reason
+
     def mark_stage_skipped(self, stage_name: str, reason: str = "") -> None:
         if stage_name not in self.history:
             self.history[stage_name] = StageOutput()
@@ -113,7 +132,7 @@ class SampleState:
         stage.verdict = Verdict.FILTER
         stage.completed_at = _now()
         if reason:
-            stage.error = reason
+            stage.skip_reason = reason
         self.verdict = SampleStatus.FILTERED
 
     def is_stage_done(self, stage_name: str) -> bool:

tests/test_claude_code_backend.py

@@ -132,14 +132,11 @@ class TestCommandConstruction:
 
 
 class TestEnvHandling:
-    def test_api_key_hidden_by_default(self):
+    def test_env_is_passed_through_untouched(self):
+        # deepzero does not strip or inject auth vars - the cli decides how to
+        # authenticate from its own config and environment
         with patch.dict("os.environ", {"ANTHROPIC_API_KEY": "sk-ant-x"}, clear=False):
             env = _backend().build_env()
-        assert "ANTHROPIC_API_KEY" not in env
-
-    def test_api_key_preserved_when_opted_out(self):
-        with patch.dict("os.environ", {"ANTHROPIC_API_KEY": "sk-ant-x"}, clear=False):
-            env = _backend(prefer_subscription_auth=False).build_env()
         assert env["ANTHROPIC_API_KEY"] == "sk-ant-x"
 
 
@@ -167,7 +164,10 @@ class TestResponseParsing:
         with patch("subprocess.run", return_value=_completed(body)):
             with pytest.raises(BackendAuthError) as exc:
                 _backend().raw_complete([{"role": "user", "content": "hi"}])
-        assert "not authenticated" in str(exc.value)
+        msg = str(exc.value)
+        assert "not authenticated" in msg
+        # relay the cli's own message plus a fixed remedy - no credential probing
+        assert "sign in" in msg
 
     def test_rate_limit_is_classified(self):
         body = _result_json(is_error=True, api_error_status=429, result="rate limit exceeded")
@@ -303,11 +303,14 @@ class TestValidation:
             errors = self._validate("claude-code")
         assert errors and "claude code cli not found" in errors[0].lower()
 
-    def test_claude_code_binding_does_not_require_api_keys(self):
-        # no ANTHROPIC_API_KEY in env, yet validation passes
-        with patch.dict("os.environ", {}, clear=True):
-            with patch(_FIND, return_value="/usr/bin/claude"):
-                assert self._validate("claude-code") == []
+    def test_claude_code_binding_does_not_require_api_keys(self, monkeypatch):
+        # no api keys anywhere, yet a valid subscription credential validates.
+        # (clears only the key vars - wiping the whole env would also remove the
+        # credential location, which is a different failure)
+        monkeypatch.delenv("ANTHROPIC_API_KEY", raising=False)
+        monkeypatch.delenv("ANTHROPIC_AUTH_TOKEN", raising=False)
+        with patch(_FIND, return_value="/usr/bin/claude"):
+            assert self._validate("claude-code") == []
 
 
 class TestAuthPreflight:

tests/test_report.py

@@ -0,0 +1,341 @@
+from __future__ import annotations
+
+import json
+
+from deepzero.engine.report import (
+    BUCKET_SUSPICIOUS,
+    BUCKET_VULNERABLE,
+    ReportConfig,
+    collect,
+    render_index,
+    write_report,
+)
+from deepzero.engine.state import RunState, SampleState, StateStore
+from deepzero.engine.types import RunStatus
+
+
+def _seed(tmp_path, *, with_findings=True, with_assessment=True, classification="vulnerable"):
+    """build a work dir shaped like a real run: one risky driver, one clean."""
+    work = tmp_path / "work" / "loldrivers"
+    store = StateStore(work)
+    store.save_run(
+        RunState(
+            run_id="run_1",
+            pipeline="loldrivers",
+            target="C:/drivers",
+            model="claude-code/opus",
+            status=RunStatus.COMPLETED,
+        )
+    )
+
+    risky = SampleState(
+        sample_id="aaa1",
+        sha256="a" * 64,
+        filename="risky.sys",
+        source_path="C:/drivers/risky.sys",
+    )
+    risky.mark_stage_completed(
+        "discover", data={"priority_score": 8.0, "dangerous_imports": ["MmMapIoSpace"]}
+    )
+    risky.mark_stage_completed(
+        "decompile",
+        artifacts={"ghidra_result": "decompiled/ghidra_result.json"},
+        data={"device_name": "RiskyDev", "function_count": 42, "ioctl_count": 2},
+    )
+    if with_findings:
+        risky.mark_stage_completed("semgrep_scanner", data={"finding_count": 2})
+    if with_assessment:
+        risky.mark_stage_completed(
+            "assess",
+            artifacts={"llm_output": "assessment.md"},
+            data={"classification": classification},
+        )
+    store.save_sample(risky)
+
+    clean = SampleState(sample_id="bbb2", filename="clean.sys", source_path="C:/drivers/clean.sys")
+    clean.mark_stage_completed("discover", data={"priority_score": 1.0})
+    store.save_sample(clean)
+
+    d = store.sample_dir("aaa1")
+    (d / "decompiled").mkdir(parents=True, exist_ok=True)
+    (d / "decompiled" / "ghidra_result.json").write_text(
+        json.dumps(
+            {
+                "success": True,
+                "device_name": "RiskyDev",
+                "symbolic_link": "\\\\DosDevices\\\\RiskyDev",
+                "ioctl_handlers": [{"code": 0x222004}, {"code": 0x222008}],
+            }
+        ),
+        encoding="utf-8",
+    )
+    if with_findings:
+        (d / "findings.json").write_text(
+            json.dumps(
+                [
+                    {
+                        "rule_id": "pipelines.loldrivers.rules.ghidra-mmmapiospace-user-controlled",
+                        "severity": "HIGH",
+                        "message": "user controlled physical map",
+                        "line_start": 42,
+                        "matched_code": "MmMapIoSpace(pa, len, 0);",
+                    },
+                    {
+                        "rule_id": "pipelines.loldrivers.rules.method-neither",
+                        "severity": "MEDIUM",
+                        "message": "METHOD_NEITHER buffer",
+                        "line_start": 88,
+                        "matched_code": "irp->UserBuffer",
+                    },
+                ]
+            ),
+            encoding="utf-8",
+        )
+    if with_assessment:
+        (d / "assessment.md").write_text(
+            "[VULNERABLE] arbitrary physical memory map via IOCTL 0x222004", encoding="utf-8"
+        )
+    return work
+
+
+class TestCollect:
+    def test_totals(self, tmp_path):
+        payload = collect(_seed(tmp_path))
+        t = payload["totals"]
+        assert t["samples"] == 2
+        assert t["total_findings"] == 2
+        assert t["with_findings"] == 1
+        assert t["assessed"] == 1
+        # severities are counted by whatever labels the findings actually use
+        assert payload["severity_totals"] == {"HIGH": 1, "MEDIUM": 1}
+
+    def test_driver_detail_is_gathered(self, tmp_path):
+        d = collect(_seed(tmp_path))["items"][0]
+        assert d.name == "risky.sys"
+        assert d.data["decompile.device_name"] == "RiskyDev"
+        assert d.data["decompile.ioctl_count"] == 2
+        assert d.data["discover.dangerous_imports"] == ["MmMapIoSpace"]
+        assert "VULNERABLE" in d.texts["llm_output"]
+        assert d.severity_counts == {"HIGH": 1, "MEDIUM": 1}
+        assert "ghidra-mmmapiospace-user-controlled" in d.rule_hits
+
+    def test_only_interesting_drivers_are_kept_in_memory(self, tmp_path):
+        payload = collect(_seed(tmp_path))
+        # the clean driver is still counted and written to csv, but needs no page
+        assert [d.sample_id for d in payload["items"]] == ["aaa1"]
+        assert len(payload["rows"]) == 2
+
+    def test_bucketing_uses_the_assessment_verdict(self, tmp_path):
+        payload = collect(_seed(tmp_path, classification="vulnerable"))
+        assert payload["items"][0].bucket == BUCKET_VULNERABLE
+        assert payload["buckets"][BUCKET_VULNERABLE] == 1
+
+    def test_findings_without_assessment_are_only_suspicious(self, tmp_path):
+        payload = collect(_seed(tmp_path, with_assessment=False))
+        assert payload["items"][0].bucket == BUCKET_SUSPICIOUS
+
+    def test_safe_verdict_is_not_flagged(self, tmp_path):
+        payload = collect(_seed(tmp_path, classification="safe"))
+        assert payload["buckets"].get(BUCKET_VULNERABLE, 0) == 0
+
+    def test_rule_totals_aggregated(self, tmp_path):
+        rt = collect(_seed(tmp_path))["rule_totals"]
+        assert rt["ghidra-mmmapiospace-user-controlled"] == 1
+        assert rt["method-neither"] == 1
+
+    def test_run_metadata(self, tmp_path):
+        run = collect(_seed(tmp_path))["run"]
+        assert run["model"] == "claude-code/opus"
+        assert run["pipeline"] == "loldrivers"
+
+    def test_safe_before_any_findings_exist(self, tmp_path):
+        payload = collect(_seed(tmp_path, with_findings=False, with_assessment=False))
+        assert payload["totals"]["total_findings"] == 0
+        assert payload["totals"]["samples"] == 2
+
+    def test_empty_work_dir_is_safe(self, tmp_path):
+        assert collect(tmp_path / "nothing")["totals"]["samples"] == 0
+
+
+class TestIndex:
+    def test_self_contained_and_offline(self, tmp_path):
+        out = render_index(collect(_seed(tmp_path)), tmp_path)
+        assert out.startswith("<!doctype html>")
+        # must open with no network: no remote assets of any kind
+        assert "http://" not in out and "https://" not in out
+        assert "<script src" not in out and "stylesheet" not in out
+
+    def test_vulnerable_is_the_headline(self, tmp_path):
+        out = render_index(collect(_seed(tmp_path)), tmp_path)
+        assert "assessed as vulnerable" in out
+        # the verdict section leads, ahead of the supporting rule breakdown
+        assert out.index("Vulnerable") < out.index("Rules that fired")
+        assert "items/aaa1.html" in out
+
+    def test_empty_buckets_are_omitted(self, tmp_path):
+        # nothing suspicious in this run, so no empty "Needs review" table
+        out = render_index(collect(_seed(tmp_path)), tmp_path)
+        assert "Needs review</h2>" not in out
+
+    def test_suspicious_section_appears_after_vulnerable(self, tmp_path):
+        work = _seed(tmp_path)
+        # add a second driver with findings but no assessment -> suspicious
+        store = StateStore(work)
+        s = SampleState(sample_id="ccc3", filename="maybe.sys", source_path="C:/drivers/maybe.sys")
+        s.mark_stage_completed("semgrep_scanner", data={"finding_count": 1})
+        store.save_sample(s)
+        (store.sample_dir("ccc3") / "findings.json").write_text(
+            json.dumps([{"rule_id": "r.x", "severity": "MEDIUM", "message": "m", "line_start": 1}]),
+            encoding="utf-8",
+        )
+        out = render_index(collect(work), tmp_path)
+        assert out.index("Vulnerable") < out.index("Needs review")
+
+
+class TestWriteReport:
+    def test_writes_the_layered_output(self, tmp_path):
+        index, json_path = write_report(_seed(tmp_path))
+        assert index.name == "index.html" and index.parent.name == "report"
+        out = index.parent
+        for name in ("inventory.csv", "findings.jsonl", "report.json"):
+            assert (out / name).exists(), name
+        summary = json.loads(json_path.read_text(encoding="utf-8"))
+        assert summary["totals"]["samples"] == 2
+        # totals only - the summary must not grow with the corpus
+        assert "items" not in summary
+
+    def test_index_stays_small_while_csv_holds_everything(self, tmp_path):
+        index, _ = write_report(_seed(tmp_path))
+        out = index.parent
+        csv_text = (out / "inventory.csv").read_text(encoding="utf-8")
+        assert "risky.sys" in csv_text and "clean.sys" in csv_text
+        pages = {p.stem for p in (out / "items").glob("*.html")}
+        assert pages == {"aaa1"}
+
+    def test_findings_are_one_json_object_per_line(self, tmp_path):
+        index, _ = write_report(_seed(tmp_path))
+        lines = [
+            ln
+            for ln in (index.parent / "findings.jsonl").read_text(encoding="utf-8").splitlines()
+            if ln
+        ]
+        assert len(lines) == 2
+        rec = json.loads(lines[0])
+        assert rec["sample_id"] == "aaa1" and rec["bucket"] == BUCKET_VULNERABLE
+        assert rec["severity"] in ("HIGH", "MEDIUM")
+
+    def test_driver_page_shows_evidence_and_links_to_artifacts(self, tmp_path):
+        index, _ = write_report(_seed(tmp_path))
+        page = (index.parent / "items" / "aaa1.html").read_text(encoding="utf-8")
+        assert "MmMapIoSpace(pa, len, 0);" in page
+        assert "llm_output" in page and "ghidra_result" in page
+        assert "all results" in page
+        # links resolve to the real artifact folder
+        assert "samples" in page
+
+    def test_untrusted_text_is_escaped_on_driver_pages(self, tmp_path):
+        work = _seed(tmp_path)
+        d = StateStore(work).sample_dir("aaa1")
+        (d / "assessment.md").write_text("<img src=x onerror=alert(1)>", encoding="utf-8")
+        index, _ = write_report(work)
+        page = (index.parent / "items" / "aaa1.html").read_text(encoding="utf-8")
+        # decompiled and LLM text is untrusted - never render it as live markup
+        assert "<img src=x onerror" not in page
+        assert "&lt;img" in page
+
+    def test_capping_detail_is_disclosed_not_silent(self, tmp_path):
+        index, _ = write_report(_seed(tmp_path), detail_limit=0)
+        text = index.read_text(encoding="utf-8")
+        assert "appear in" in text and "inventory.csv" in text
+
+    def test_custom_out_dir(self, tmp_path):
+        out = tmp_path / "elsewhere"
+        index, _ = write_report(_seed(tmp_path), out)
+        assert index.parent == out
+
+    def test_regenerating_overwrites(self, tmp_path):
+        work = _seed(tmp_path)
+        write_report(work)
+        index, _ = write_report(work)
+        assert index.read_text(encoding="utf-8").count("<!doctype html>") == 1
+
+
+class TestPipelineAgnostic:
+    """a completely different pipeline must render without code changes."""
+
+    def _github_run(self, tmp_path):
+        work = tmp_path / "work" / "srchunt"
+        store = StateStore(work)
+        store.save_run(
+            RunState(
+                run_id="run_9",
+                pipeline="srchunt",
+                target="github.com/acme",
+                model="claude-code/opus",
+                status=RunStatus.COMPLETED,
+            )
+        )
+        repo = SampleState(sample_id="r1", filename="acme/api", source_path="github.com/acme/api")
+        repo.mark_stage_completed("discover", data={"stars": 4200, "language": "go"})
+        repo.mark_stage_completed(
+            "sast", data={"finding_count": 1}, artifacts={"sast": "sast.json"}
+        )
+        repo.mark_stage_completed("triage", data={"verdict": "exploitable"})
+        store.save_sample(repo)
+        (store.sample_dir("r1") / "sast.json").write_text(
+            json.dumps(
+                [
+                    {
+                        "id": "go.sql-injection",
+                        "level": "critical",
+                        "title": "SQL injection in query builder",
+                        "path": "internal/db/query.go",
+                        "start_line": 88,
+                        "snippet": 'db.Raw("SELECT " + userInput)',
+                    }
+                ]
+            ),
+            encoding="utf-8",
+        )
+        return work
+
+    def test_declared_config_shapes_the_report(self, tmp_path):
+        work = self._github_run(tmp_path)
+        cfg = {
+            "title": "Acme source review",
+            "entity": "repository",
+            "classification_key": "verdict",
+            "vulnerable_when": ["exploitable"],
+            "columns": ["discover.stars", "discover.language"],
+            "findings_files": ["sast.json"],
+        }
+        index, json_path = write_report(work, config=cfg)
+        text = index.read_text(encoding="utf-8")
+
+        # the pipeline's own vocabulary and verdict key drive the page
+        assert "Acme source review" in text
+        assert "repository" in text and "repositorys" not in text.replace("repositorys", "")
+        assert "assessed as vulnerable" in text
+        # its own severity vocabulary is preserved, not remapped to a fixed set
+        assert "CRITICAL" in json.loads(json_path.read_text(encoding="utf-8"))["severity_totals"]
+        # declared columns appear as chips/columns
+        assert "stars" in text and "4200" in text
+
+    def test_works_with_no_config_at_all(self, tmp_path):
+        work = self._github_run(tmp_path)
+        index, _ = write_report(work)
+        text = index.read_text(encoding="utf-8")
+        # default entity wording, and the finding is still surfaced for review
+        assert "sample" in text
+        # no verdict key configured, so it lands in review rather than confirmed
+        assert "Needs review" in text
+
+    def test_alien_finding_shape_is_normalized(self, tmp_path):
+        work = self._github_run(tmp_path)
+        payload = collect(work, config=ReportConfig.from_dict({"findings_files": ["sast.json"]}))
+        f = payload["items"][0].findings[0]
+        assert f["severity"] == "CRITICAL"
+        assert f["rule_id"] == "go.sql-injection"
+        assert "SQL injection" in f["message"]
+        assert f["location"] == "internal/db/query.go"
+        assert f["line"] == 88

tests/test_runner.py

@@ -5,6 +5,7 @@ from pathlib import Path
 from deepzero.engine.runner import PipelineRunner
 from deepzero.engine.stage import (
     BulkMapProcessor,
+    IngestProcessor,
     MapProcessor,
     ProcessorContext,
     ProcessorEntry,
@@ -334,3 +335,87 @@ class TestResolveParallelism:
         proc = self._NoCeilingProc(StageSpec(name="d", processor="x"))
         spec = StageSpec(name="d", processor="x", parallel=0)
         assert PipelineRunner._resolve_parallelism(None, spec, proc) == 8
+
+
+class TestCachedSamplesStayInThePipeline:
+    """a sample whose work was already done still flows to the following
+    stages. skipping work is not the same as filtering the sample out: a
+    resumed run must analyse exactly what a fresh run would."""
+
+    class _AlreadyDone(MapProcessor):
+        def should_skip(self, ctx, entry):
+            return "output already cached"
+
+        def process(self, ctx, entry):
+            raise AssertionError("process() must not run when should_skip returns a reason")
+
+    class _Counting(MapProcessor):
+        seen: list = []
+
+        def process(self, ctx, entry):
+            type(self).seen.append(entry.sample_id)
+            return ProcessorResult.ok(data={"ran": True})
+
+    def test_cached_stage_is_completed_not_filtered(self, tmp_path):
+        from deepzero.engine.state import SampleState
+        from deepzero.engine.types import SampleStatus, StageStatus, Verdict
+
+        state = SampleState(sample_id="s1", filename="a.sys")
+        state.mark_stage_cached("decompile", "output already cached")
+
+        out = state.history["decompile"]
+        assert out.status == StageStatus.COMPLETED
+        assert out.verdict == Verdict.CONTINUE
+        assert out.skip_reason == "output already cached"
+        # a skip reason is not an error
+        assert out.error is None
+        # and the sample is still eligible for later stages
+        assert state.verdict != SampleStatus.FILTERED
+
+    def test_skip_reason_is_not_stored_as_an_error(self, tmp_path):
+        from deepzero.engine.state import SampleState
+
+        state = SampleState(sample_id="s1", filename="a.sys")
+        state.mark_stage_skipped("kernel_filter", "not a kernel driver")
+        out = state.history["kernel_filter"]
+        assert out.skip_reason == "not a kernel driver"
+        assert out.error is None
+
+    def test_downstream_stage_still_sees_a_cached_sample(self, tmp_path):
+        type(self._Counting).seen = []
+        self._Counting.seen = []
+        store = StateStore(tmp_path / "work")
+        run = RunState(run_id="r1", pipeline="p")
+        store.save_run(run)
+
+        target = tmp_path / "a.sys"
+        target.write_bytes(b"MZ")
+
+        class OneSample(IngestProcessor):
+            def __init__(self):
+                self.spec = StageSpec(name="discover", processor="i")
+                self.config = {}
+
+            def setup(self, global_config):
+                pass
+
+            def process(self, ctx, t):
+                return [Sample(sample_id="s1", source_path=target, filename="a.sys")]
+
+        cached_spec = StageSpec(name="decompile", processor="x")
+        after_spec = StageSpec(name="scan", processor="y")
+        after = self._Counting(after_spec)
+
+        runner = PipelineRunner(
+            ingest=OneSample(),
+            stages=[(cached_spec, self._AlreadyDone(cached_spec)), (after_spec, after)],
+            state_store=store,
+            pipeline_dir=tmp_path,
+            global_config={},
+        )
+        runner.run(tmp_path, run)
+
+        # the whole point: the cached sample reached the next stage
+        assert after.seen == ["s1"], "cached sample was dropped before the next stage"
+        final = store.load_sample("s1")
+        assert "scan" in final.history

tests/test_semgrep_scanner.py

@@ -24,8 +24,8 @@ class TestRulesPathResolution:
         )
 
     def test_validate_and_process_resolve_the_same_path(self, tmp_path, monkeypatch):
-        # regression: validate() approved a cwd-relative path while process()
-        # used a pipeline_dir-relative one, so the scan ran with no rules.
+        # the check that approves a run and the run itself must agree on where
+        # the rules live, otherwise a scan can start with no rules loaded.
         # pin cwd so the cwd-relative "rules" resolves deterministically.
         monkeypatch.chdir(tmp_path)
         rules = tmp_path / "rules"