delivery-friction-analyzer 0.21.2 → 0.22.1

package/README.md

@@ -131,7 +131,7 @@ Each ranked bottleneck example includes source references, workflow-run conclusi
 
 Use `--source sample` for the bundled synthetic tutorial data. Use `--source github` for live repository analysis. Existing live commands that pass `--repo`, `--profile`, or `--limit` without `--source` still run as GitHub analysis, but new users should prefer the explicit source flag.
 
-Use `--dry-run` or `--metadata-only` to validate repository access, profile JSON, output directory writability, and sampled API coverage without writing full report artifacts. The output directory may be created during this check, and a temporary probe file may be written and removed.
+Use `--dry-run` or `--metadata-only` with `--source github` to run a live GitHub coverage probe that validates repository access, profile JSON, output directory writability, and sampled API coverage without writing full report artifacts. The output directory may be created during this check, and a temporary probe file may be written and removed.
 
 Use `--no-csv` when you want the Markdown, JSON, source, normalized, metrics, and methodology artifacts without spreadsheet-friendly CSV exports.
 
@@ -139,7 +139,7 @@ Use `--exclude-pr-class <class>` to remove a configured PR class from downstream
 
 Use `--json` when automation needs the full machine-readable completion receipt on stdout.
 
-Use `--interactive` only in a terminal when you want prompts. When combined with `--json`, prompts and progress stay off stdout so the final completion receipt remains parseable JSON.
+Use `--interactive` only in a terminal when you want prompts for live GitHub setup. Enter `?` at supported prompts for contextual help without restarting the flow. When combined with `--json`, prompts and progress stay off stdout so the final completion receipt remains parseable JSON.
 
 ## How To Read A Report
 

package/docs/contracts/friction-report.md

@@ -28,7 +28,7 @@ The command reads local `friction-metrics.v1` JSON and writes deterministic `fri
 - `source`: optional source-bundle provenance copied into live-generated report
   artifacts, including `kind` and a human-readable label.
 - `targetRepository`: analyzed repository identity; live analysis sample size is encoded as `targetRepository.analysisPullRequestLimit` from collection metadata.
-- `analysisFilter`: optional metadata for explicit filters applied before metrics computation, including excluded PR classes and before/after PR counts.
+- `analysisFilter`: optional metadata for explicit filters applied before metrics computation, including excluded PR classes and before/after PR counts. Live dry-run completion receipts may also include requested `analysisFilter.excludedPrClasses` with null before/after counts because dry-run coverage probes do not compute filtered metrics or report artifacts.
 - `configuredWorkflow`: optional user-configured workflow context from the repository profile. It is not observed GitHub evidence and does not change scoring, ranking, CSV exports, or PR class matching.
 - `contributorSource`: optional sanitized contributor-source metadata from the repository profile and collection path. It records source type, path, coverage status, parsed hint count, and guardrail note. It does not include raw contributor file contents or contributor rankings.
 - `collectionCoverage`: optional source collection coverage metadata copied into live-generated report JSON artifacts. `collectionCoverage.status` records aggregate coverage, and `collectionCoverage.sourceFamilies` lists source-family entries with `family`, `status`, `attempts`, `source`, `diagnostics`, and `downstreamImpact`. This uses the generic `source-bundle.v1` `coverage.sourceFamilies` name; legacy GitHub `apiFamilies` is not a live `friction-report.v1` field.
@@ -128,7 +128,7 @@ Full live analysis writes `methodology.md` as a hybrid artifact: stable explanat
 
 The methodology artifact should stay aligned with this contract and the Markdown methodology summary, but it may be more detailed than the main report.
 
-When PR class filtering is applied, `source-bundle.json` remains the full collected sample, while `normalized.json`, `metrics-summary.json`, `friction-report.json`, `friction-report.md`, `methodology.md`, and CSV exports describe the filtered sample. The methodology and CLI completion output must name the excluded PR classes and show the filtered PR count. If filtering excludes every collected PR, the analysis must fail without writing complete-looking empty reports.
+When PR class filtering is applied to a full analysis, `source-bundle.json` remains the full collected sample, while `normalized.json`, `metrics-summary.json`, `friction-report.json`, `friction-report.md`, `methodology.md`, and CSV exports describe the filtered sample. The methodology and CLI completion output must name the excluded PR classes and show the filtered PR count. If filtering excludes every collected PR, the analysis must fail without writing complete-looking empty reports. Live dry-run receipts record requested PR class exclusions without a filtered count because dry-run does not build normalized metrics.
 
 ## CSV Evidence Exports
 
@@ -143,7 +143,7 @@ Minimum CSV column groups:
 - `comment-sources.csv`: source name, total comments, bot/scanner classification, human/author classification, and share of all comments.
 - `collection-coverage.csv`: source family, status, attempts, source label, diagnostics, and downstream impact.
 
-Empty CSV cells mean unavailable or not applicable. Numeric zero should be used only for observed or computed zero counts. Count columns that depend on optional GitHub coverage should keep source or coverage labels nearby so spreadsheet readers can tell unavailable evidence apart from observed zeroes. CSVs must not include raw comment bodies, raw workflow logs, tokens, secret-bearing environment details, or individual contributor/reviewer rankings.
+Empty CSV cells mean unavailable or not applicable. Numeric zero should be used only for observed or computed zero counts. Count columns that depend on optional GitHub or sample-bundle coverage should keep source or coverage labels nearby so spreadsheet readers can tell unavailable evidence apart from observed zeroes. `pr-metrics.csv` `review_threads` is populated when normalized review-thread source evidence is available, including synthetic sample evidence and live GraphQL review-thread evidence. CSVs must not include raw comment bodies, raw workflow logs, tokens, secret-bearing environment details, or individual contributor/reviewer rankings.
 
 Contributor-source coverage appears in `collection-coverage.csv` as the `contributor_source` source family when configured. CSVs may include aggregate comment-source counts influenced by contributor hints, but they must not include raw `.all-contributorsrc` contents, contributor names, contributor login lists, or person rankings.
 

package/docs/reference/run-presets.md

@@ -1,14 +1,14 @@
 # Run Presets
 
-Run presets are optional local JSON files for reusing CLI run settings. They are intended for rerunning the same analysis without re-answering interactive prompts.
+Run presets are optional local JSON files for reusing live GitHub CLI run settings. They are intended for rerunning the same live analysis without re-answering interactive prompts. The bundled `--source sample` tutorial path does not save or load presets.
 
-Repository meaning stays in repository profiles. Put file rules, PR class rules, workflow context, branch or release strategy, and contributor-source declarations in a repository profile. A run preset may only point at a profile and store run inputs or preferences such as the target repository, sample size, output directory, dry-run mode, CSV preference, JSON completion preference, validation-target mode, and requested PR class exclusions.
+Repository meaning stays in repository profiles. Put file rules, PR class rules, workflow context, branch or release strategy, and contributor-source declarations in a repository profile. A run preset may only point at a profile and store live run inputs or preferences such as the target repository, pull request limit, output directory, dry-run coverage-probe mode, CSV preference, JSON completion preference, validation-target mode, and requested PR class exclusions.
 
 When a preset supplies `profilePath`, the CLI validates that referenced profile exactly as if it had been passed with `--profile`. Presets do not copy, freeze, or override profile rules; fixing profile validation failures means editing the referenced profile or choosing a different profile path.
 
 ## Save A Preset
 
-Interactive setup asks whether to save a local run preset near the end of the prompt flow. If you answer yes, you choose the preset path explicitly. The CLI does not invent a global or cloud-synced preset location.
+Interactive live GitHub setup asks whether to save a local run preset near the end of the prompt flow. If you answer yes, you choose the preset path explicitly. The CLI does not invent a global or cloud-synced preset location.
 
 Saving a preset may overwrite an existing regular file at that path, but the path must not be a directory, symbolic link, or other special file.
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "delivery-friction-analyzer",
-  "version": "0.21.2",
+  "version": "0.22.1",
   "description": "Local GitHub pull request analytics for delivery friction reports.",
   "license": "MIT",
   "type": "module",

package/release-log.md

@@ -2,6 +2,22 @@
 
 ## Unreleased
 
+### 2026-06-28 — CLI Artifact Truthfulness
+
+- What changed: Live dry-run JSON receipts now show requested PR-class exclusions without implying filtered metrics were computed, and `pr-metrics.csv` fills `review_threads` when sample or live review-thread evidence is available.
+- Why it matters: Maintainers and scripts can trust completion receipts and CSV evidence to reflect accepted filters and available review-thread counts.
+- Who is affected: Maintainers and users reading JSON completion receipts, CSV exports, and contract docs from sample or live GitHub analysis.
+- Action needed: None.
+- PR: https://github.com/hannasdev/delivery-friction-analyzer/pull/68
+
+### 2026-06-28 — CLI Command Help Clarity
+
+- What changed: CLI help now separates the bundled sample, live GitHub analysis, live coverage probes, output controls, interactive setup, and reusable live-run presets, with mode-specific help for `--source sample --help` and `--source github --help`.
+- Why it matters: First-time users and maintainers can choose the right workflow before running into rejected flag combinations, and interactive setup can explain supported prompts without restarting the flow.
+- Who is affected: Users trying the bundled sample, maintainers running live GitHub analysis or dry-run coverage probes, and contributors reviewing CLI setup behavior.
+- Action needed: None.
+- PR: https://github.com/hannasdev/delivery-friction-analyzer/pull/67
+
 ### 2026-06-27 — First-Run Profile Prompt Clarity
 
 - What changed: Interactive GitHub setup now explains starter-profile limitations, gives clearer guidance before adding Conventional Commit PR class rules, and only prints the starter-profile completion reminder when a new profile was created.

package/src/cli/analyze-github.js

@@ -135,30 +135,84 @@ const CSV_ARTIFACT_KEYS = new Set([
 export const USAGE = `Usage:
   delivery-friction-analyzer --source sample --out <directory>
   delivery-friction-analyzer --source github --repo <owner/name> --limit <1-100> --profile <path> --out <directory>
-  delivery-friction-analyzer --repo <owner/name> --limit <1-100> --profile <path> --out <directory>
-  delivery-friction-analyzer --repo <owner/name> --limit <1-100> --profile <path> --out <directory> --dry-run
 
-Options:
-  --source <sample|github> Choose the bundled synthetic sample or live GitHub analysis.
+Workflows:
+  Sample tutorial:
+    Uses bundled synthetic data. Accepts output controls only.
+    delivery-friction-analyzer --source sample --out reports/tutorial
+
+  Live GitHub analysis:
+    Collects repository data from GitHub using a repository profile.
+    delivery-friction-analyzer --source github --repo owner/name --limit 30 --profile path/to/profile.json --out reports/owner-name
+
+  Live GitHub coverage probe:
+    --dry-run and --metadata-only validate live GitHub access, profile JSON, output writability, and sampled API coverage without report artifacts.
+    delivery-friction-analyzer --source github --repo owner/name --limit 30 --profile path/to/profile.json --out reports/owner-name --dry-run
+
+Output controls:
+  --out <directory>         Output directory for generated artifacts.
+  --json                    Print the machine-readable completion receipt to stdout.
+  --no-json                 Disable JSON completion output.
+  --csv                     Enable curated CSV evidence exports when a preset disabled them.
+  --no-csv                  Suppress curated CSV evidence exports.
+
+Help:
+  --source sample --help    Show sample-mode options.
+  --source github --help    Show live GitHub, dry-run, interactive, and preset options.
+`;
+
+export const SAMPLE_USAGE = `Usage:
+  delivery-friction-analyzer --source sample --out <directory>
+
+Sample tutorial:
+  Uses bundled synthetic data and never calls GitHub.
+  Sample mode writes the same report bundle shape as a live analysis for tutorial use.
+
+Sample output controls:
+  --out <directory>         Required output directory for generated sample artifacts.
+  --json                    Print the machine-readable completion receipt to stdout.
+  --no-json                 Disable JSON completion output.
+  --csv                     Enable curated CSV evidence exports.
+  --no-csv                  Suppress curated CSV evidence exports.
+
+Live-only flags are not supported with --source sample:
+  --repo, --limit, --profile, --dry-run, --metadata-only, --validation-target,
+  --interactive, --preset, --save-preset, --exclude-pr-class, --allow-product-repository
+`;
+
+export const GITHUB_USAGE = `Usage:
+  delivery-friction-analyzer --source github --repo <owner/name> --limit <1-100> --profile <path> --out <directory>
+  delivery-friction-analyzer --source github --repo <owner/name> --limit <1-100> --profile <path> --out <directory> --dry-run
+  delivery-friction-analyzer --interactive --source github
+
+Live GitHub analysis:
   --repo <owner/name>       Target GitHub repository to analyze.
   --limit <1-100>           Latest merged pull request count.
   --profile <path>          Repository profile JSON used for file role classification.
   --out <directory>         Output directory for generated artifacts.
-  --dry-run                 Validate inputs and sample GitHub coverage without writing artifacts.
-  --no-dry-run              Disable dry-run mode when a preset enabled it.
+
+Live GitHub coverage probes:
+  --dry-run                 Validate live GitHub access, profile JSON, output writability, and sampled API coverage without writing report artifacts.
   --metadata-only           Alias for --dry-run.
+  --no-dry-run              Disable dry-run mode when a preset enabled it.
+
+Live filters and metadata:
   --validation-target       Mark output metadata as an internal validation run; does not bypass target validation.
   --no-validation-target    Disable validation-target mode when a preset enabled it.
   --allow-product-repository
                             Explicit live-analysis override for intentional self-analysis of this product repository.
-  --exclude-pr-class <cls>  Exclude a PR class from normalized, metrics, report, methodology, and CSV artifacts. Repeat or comma-separate values.
-  --csv                     Enable curated CSV evidence exports when a preset disabled them.
-  --no-csv                  Suppress curated CSV evidence exports.
+  --exclude-pr-class <cls>  Exclude a configured PR class from downstream normalized, metrics, report, methodology, and CSV artifacts. Repeat or comma-separate values.
+
+Output controls:
   --json                    Print the machine-readable completion receipt to stdout.
   --no-json                 Disable JSON completion output when a preset enabled it.
-  --interactive             Prompt for missing run options in a terminal.
-  --preset <path>           Load local run settings from a saved preset. Explicit CLI flags override preset values.
-  --save-preset <path>      Save local run settings for non-interactive reruns.
+  --csv                     Enable curated CSV evidence exports when a preset disabled them.
+  --no-csv                  Suppress curated CSV evidence exports.
+
+Interactive setup and presets:
+  --interactive             Prompt for missing live GitHub run options in a terminal; enter ? at supported prompts for contextual help.
+  --preset <path>           Load reusable live GitHub run settings from a saved preset. Explicit CLI flags override preset values.
+  --save-preset <path>      Save reusable live GitHub run settings for non-interactive reruns.
 `;
 
 export const SOURCE_SELECTION_GUIDANCE = `Choose what to analyze.
@@ -199,6 +253,13 @@ function explicitCliOptionKeys(argv) {
 }
 
 export function parseAnalyzeGithubArgs(argv) {
+  if (hasHelpOption(argv)) {
+    const parsed = { help: true };
+    const source = sourceForHelp(argv);
+    if (source !== undefined) parsed.source = source;
+    return attachOptionSource(parsed, "explicitCliOptions", new Set(source === undefined ? [] : ["source"]));
+  }
+
   const options = {
     dryRun: false,
     isValidationTarget: false,
@@ -209,9 +270,6 @@ export function parseAnalyzeGithubArgs(argv) {
   const explicitOptions = explicitCliOptionKeys(argv);
   for (let index = 0; index < argv.length; index += 1) {
     const arg = argv[index];
-    if (arg === "--help" || arg === "-h") {
-      return { help: true };
-    }
     if (!arg.startsWith("--")) {
       throw new Error(`Unexpected argument: ${arg}`);
     }
@@ -268,6 +326,25 @@ export function parseAnalyzeGithubArgs(argv) {
   return attachOptionSource(parsed, "explicitCliOptions", explicitOptions);
 }
 
+function hasHelpOption(argv) {
+  return argv.includes("--help") || argv.includes("-h");
+}
+
+function sourceForHelp(argv) {
+  for (let index = 0; index < argv.length; index += 1) {
+    if (argv[index] !== "--source") continue;
+    const source = argv[index + 1];
+    if (source === "sample" || source === "github") return source;
+  }
+  return undefined;
+}
+
+function usageForOptions(options) {
+  if (options?.source === "sample") return SAMPLE_USAGE;
+  if (options?.source === "github") return GITHUB_USAGE;
+  return USAGE;
+}
+
 function normalizeExcludedPrClasses(values) {
   return [...new Set(values
     .flatMap(value => String(value).split(","))
@@ -537,7 +614,7 @@ function rejectSampleLiveOptions(options) {
     incompatible.push("--exclude-pr-class");
   }
   if (!incompatible.length) return;
-  throw new Error(`--source sample cannot be combined with live GitHub option(s): ${incompatible.join(", ")}. Use only output options such as --out, --json, --csv, or --no-csv.`);
+  throw new Error(`--source sample cannot be combined with live GitHub option(s): ${incompatible.join(", ")}. Allowed sample output controls are --out, --json, --no-json, --csv, and --no-csv. Use --source github for live repository, dry-run, interactive, preset, validation, and PR-class filtering options.`);
 }
 
 function targetInputFromRepositorySlug(repository) {
@@ -590,21 +667,22 @@ function formatChoiceList(choices) {
 }
 
 function formatInteractivePrompt(prompt) {
+  const helpSuffix = prompt.help ? " Enter ? for help" : "";
   const suffix = prompt.defaultValue === undefined
     ? ""
     : Array.isArray(prompt.defaultValue)
       ? (prompt.defaultValue.length ? ` [${prompt.defaultValue.join(",")}]` : "")
       : ` [${prompt.defaultValue}]`;
   if (prompt.type === "confirm") {
-    return `${prompt.message}${prompt.defaultValue ? " [Y/n]" : " [y/N]"} `;
+    return `${prompt.message}${helpSuffix}${prompt.defaultValue ? " [Y/n]" : " [y/N]"} `;
   }
   if (prompt.type === "multi-select" && prompt.choices?.length) {
-    return `${prompt.message} (${prompt.choices.map(choiceValue).join(",")})${suffix}: `;
+    return `${prompt.message}${helpSuffix} (${prompt.choices.map(choiceValue).join(",")})${suffix}: `;
   }
   if (prompt.type === "select" && prompt.choices?.length) {
-    return `${prompt.message}\n${formatChoiceList(prompt.choices)}\nChoose a number or identifier${suffix}: `;
+    return `${prompt.message}${helpSuffix}\n${formatChoiceList(prompt.choices)}\nChoose a number or identifier${suffix}: `;
   }
-  return `${prompt.message}${suffix}: `;
+  return `${prompt.message}${helpSuffix}${suffix}: `;
 }
 
 function createTerminalPromptAdapter({ input, output }) {
@@ -632,6 +710,16 @@ async function callPromptAdapter(promptAdapter, prompt) {
 async function askUntilValid(promptAdapter, prompt, { normalize, validate, output }) {
   for (;;) {
     const raw = await callPromptAdapter(promptAdapter, prompt);
+    if (String(raw ?? "").trim() === "?" && prompt.help) {
+      if (typeof promptAdapter.writeHelp === "function") {
+        promptAdapter.writeHelp(prompt.help);
+      } else if (typeof promptAdapter.writeError === "function") {
+        promptAdapter.writeError(prompt.help);
+      } else if (output?.write) {
+        output.write(`${prompt.help}\n`);
+      }
+      continue;
+    }
     try {
       const value = normalize(raw, prompt);
       await validate(value);
@@ -950,6 +1038,7 @@ async function promptConventionalCommitPrClassPreset(promptAdapter, output, prof
     id: "addConventionalCommitPrClasses",
     type: "confirm",
     message,
+    help: "Optional profile setup: add reusable title rules when Conventional Commit prefixes match this repository. This changes profile classification only, not scoring or GitHub collection.",
     defaultValue: false,
   }, {
     output,
@@ -991,6 +1080,7 @@ async function promptWorkflowField(promptAdapter, output, { id, message, choices
     id,
     type: "select",
     message,
+    help: "Workflow context is configured profile metadata. Choose the closest stable repository practice; it helps report interpretation but is not observed GitHub evidence.",
     choices: workflowChoices(choices),
     defaultValue,
   }, {
@@ -1030,6 +1120,7 @@ async function promptWorkflowProfileUpdate(promptAdapter, output, profile, { isN
       id: "releasePrTitleIncludes",
       type: "text",
       message: `Release PR title includes (blank to skip PR class rule; suggested: ${suggestedReleaseTitle})`,
+      help: "Use this only when release PR titles follow a stable phrase. Blank skips the generated release PR class rule.",
     }, {
       output,
       normalize: normalizeTextAnswer,
@@ -1044,6 +1135,7 @@ async function promptWorkflowProfileUpdate(promptAdapter, output, profile, { isN
           id: "updateReleasePrClass",
           type: "confirm",
           message: "Update existing title-based release PR class rule",
+          help: "Updates the existing title-based release PR class rule in the repository profile. Existing unrelated profile rules are kept.",
           defaultValue: false,
         }, {
           output,
@@ -1065,6 +1157,7 @@ async function promptWorkflowProfileUpdate(promptAdapter, output, profile, { isN
             id: "addReleasePrClass",
             type: "confirm",
             message: "Add release PR class rule from title convention",
+            help: "Adds a title-based release PR class rule to the repository profile when that convention matches this repository.",
             defaultValue: true,
           }, {
             output,
@@ -1097,6 +1190,7 @@ async function maybeConfigureInteractiveProfile(promptAdapter, output, profileSt
       id: "createProfile",
       type: "confirm",
       message: `Create repository profile at this path. ${STARTER_PROFILE_PROMPT_COPY}`,
+      help: "A repository profile is required for live GitHub analysis. Interactive setup can create a starter profile at the path you entered, then you can review or refine it before a full run.",
       defaultValue: true,
     }, {
       output,
@@ -1111,6 +1205,7 @@ async function maybeConfigureInteractiveProfile(promptAdapter, output, profileSt
       id: "configureWorkflow",
       type: "confirm",
       message: "Configure repository workflow profile fields",
+      help: "Workflow profile fields are configured context for report interpretation. Choose yes to review merge, release, and branch strategy prompts; choose no to keep the existing profile values.",
       defaultValue: false,
     }, {
       output,
@@ -1220,6 +1315,7 @@ export async function collectInteractiveAnalyzeGithubOptions(options, {
         id: "repository",
         type: "text",
         message: "Target GitHub repository",
+        help: "Enter the live GitHub repository as owner/name. Sample mode is not part of interactive setup; use --source sample --out <directory> for the bundled tutorial.",
       }, {
         output,
         normalize: normalizeTextAnswer,
@@ -1232,6 +1328,7 @@ export async function collectInteractiveAnalyzeGithubOptions(options, {
         id: "limit",
         type: "integer",
         message: "Latest merged pull request count",
+        help: "Choose how many recent merged pull requests to collect from live GitHub. Smaller limits are faster; larger limits give reports more evidence.",
         defaultValue: 30,
       }, {
         output,
@@ -1245,6 +1342,7 @@ export async function collectInteractiveAnalyzeGithubOptions(options, {
         id: "profilePath",
         type: "path",
         message: "Repository profile path",
+        help: "Enter a local repository-profile.v1 JSON path. If the path does not exist, interactive setup can create a starter profile there.",
       });
       profileState = prompted;
     } else {
@@ -1284,6 +1382,7 @@ export async function collectInteractiveAnalyzeGithubOptions(options, {
         id: "outDir",
         type: "path",
         message: "Output directory",
+        help: "Choose where generated artifacts or dry-run probe files should be written. Interactive setup may create the directory and check that it is writable.",
         defaultValue: defaultOutDirForRepository(resolved.repository),
       }, {
         output,
@@ -1299,7 +1398,8 @@ export async function collectInteractiveAnalyzeGithubOptions(options, {
       resolved.dryRun = await askUntilValid(adapter, {
         id: "dryRun",
         type: "confirm",
-        message: "Run metadata-only dry run",
+        message: "Run live GitHub metadata-only coverage probe",
+        help: "A dry run is a live GitHub coverage probe. It validates access, profile JSON, output writability, and sampled API coverage without writing report artifacts.",
         defaultValue: false,
       }, {
         output,
@@ -1314,6 +1414,7 @@ export async function collectInteractiveAnalyzeGithubOptions(options, {
         id: "csv",
         type: "confirm",
         message: "Write CSV evidence files",
+        help: "CSV evidence files are optional spreadsheet-friendly artifacts for full report runs. They are not written during dry-run coverage probes.",
         defaultValue: true,
       }, {
         output,
@@ -1328,6 +1429,7 @@ export async function collectInteractiveAnalyzeGithubOptions(options, {
         id: "json",
         type: "confirm",
         message: "Print completion as JSON",
+        help: "JSON completion writes the final machine-readable receipt to stdout. Prompts and progress stay on stderr so automation can parse stdout.",
         defaultValue: false,
       }, {
         output,
@@ -1344,6 +1446,7 @@ export async function collectInteractiveAnalyzeGithubOptions(options, {
           id: "excludedPrClasses",
           type: "multi-select",
           message: "Exclude PR classes (comma-separated, blank for none)",
+          help: "Optionally exclude configured PR classes from downstream normalized data, metrics, reports, methodology, and CSV artifacts. The source bundle still preserves the full collected sample.",
           choices: availablePrClasses,
           defaultValue: [],
         }, {
@@ -1362,6 +1465,7 @@ export async function collectInteractiveAnalyzeGithubOptions(options, {
         id: "saveRunPreset",
         type: "confirm",
         message: "Save local run preset for non-interactive reruns",
+        help: "Run presets store reusable live GitHub run settings such as repo, profile, limit, output, dry-run preference, JSON/CSV preference, and requested PR class exclusions. Sample mode does not save or load presets.",
         defaultValue: false,
       }, {
         output,
@@ -1373,6 +1477,7 @@ export async function collectInteractiveAnalyzeGithubOptions(options, {
           id: "runPresetPath",
           type: "path",
           message: "Run preset path",
+          help: "Choose a local JSON file path for reusable live GitHub run settings. The path must be a regular file path, not a directory or symlink.",
         }, {
           output,
           normalize: normalizeTextAnswer,
@@ -1590,6 +1695,15 @@ function summarizeResult({ dryRun, outDir, paths, sourceBundle, metrics, report,
   return summary;
 }
 
+function requestedAnalysisFilter(excludedPrClasses = []) {
+  if (!excludedPrClasses.length) return null;
+  return {
+    excludedPrClasses,
+    originalPullRequests: null,
+    filteredPullRequests: null,
+  };
+}
+
 function applyPrClassFilter(normalized, excludedPrClasses = []) {
   if (!excludedPrClasses.length) return normalized;
   const excluded = new Set(excludedPrClasses);
@@ -1719,7 +1833,7 @@ export async function runAnalyzeGithub(options, {
       requestedLimit: options.limit,
       sampledLimit: collectionLimit,
       csv: false,
-      analysisFilter: null,
+      analysisFilter: requestedAnalysisFilter(options.excludedPrClasses ?? []),
       savedProfilePath: options.savedProfilePath,
       savedRunPresetPath: options.savedRunPresetPath,
       prClassRulesWritten: options.prClassRulesWritten,
@@ -1883,10 +1997,13 @@ export function formatAnalyzeGithubCompletion(result) {
   }
 
   if (result.analysisFilter?.excludedPrClasses?.length) {
-    lines.push(
-      `Analysis filter: excluded PR class(es): ${result.analysisFilter.excludedPrClasses.join(", ")}.`,
-      `Filtered sample: ${result.analysisFilter.filteredPullRequests} of ${result.analysisFilter.originalPullRequests} collected pull request(s).`,
-    );
+    lines.push(`Analysis filter: excluded PR class(es): ${result.analysisFilter.excludedPrClasses.join(", ")}.`);
+    if (Number.isInteger(result.analysisFilter.filteredPullRequests)
+      && Number.isInteger(result.analysisFilter.originalPullRequests)) {
+      lines.push(`Filtered sample: ${result.analysisFilter.filteredPullRequests} of ${result.analysisFilter.originalPullRequests} collected pull request(s).`);
+    } else if (result.dryRun) {
+      lines.push("Filter application: requested only; dry-run coverage probes do not compute filtered metrics or report artifacts.");
+    }
   }
 
   if (result.savedProfilePath) {
@@ -1938,7 +2055,7 @@ export async function runAnalyzeGithubCli(argv, {
   try {
     const parsedOptions = parseAnalyzeGithubArgs(argv);
     if (parsedOptions.help) {
-      stdout.write(USAGE);
+      stdout.write(usageForOptions(parsedOptions));
       return null;
     }
     if (parsedOptions.source !== undefined) {

package/src/report/evidence-artifacts.js

@@ -94,9 +94,12 @@ function hasObservedWorkflowRuns(workflowRuns = {}) {
   return (workflowRuns.coverage ?? workflowRuns.workflowRunCoverage) === "observed";
 }
 
-function hasObservedReviewThreads(reviewThreads = {}) {
+function hasObservedReviewThreads(reviewThreads = {}, coverage = {}) {
   const source = reviewThreads.source ?? reviewThreads.reviewThreadSource ?? "unavailable";
-  return String(source).startsWith("graphql");
+  if (String(source).startsWith("graphql")) return true;
+  if (String(source).startsWith("not_sampled") || source === "unavailable") return false;
+  if (String(source).includes("review_threads")) return true;
+  return coverage.status === "available";
 }
 
 function hasObservedReviewDecision(reviewDecision = {}) {
@@ -135,7 +138,7 @@ function prMetricsCsv(metricsSummary, analysisFilter) {
     ...SCORE_COLUMNS.map(([header]) => header),
   ];
   const rows = sortedPullRequests(metricsSummary).map(pr => {
-    const observedReviewThreads = hasObservedReviewThreads(pr.review?.threads);
+    const observedReviewThreads = hasObservedReviewThreads(pr.review?.threads, pr.coverage?.reviewThreads);
     const observedReviewDecision = hasObservedReviewDecision(pr.review?.decision);
     const observedWorkflowRuns = hasObservedWorkflowRuns(pr.ci?.workflowRuns);
     const row = {