fix: stop issues --overview noise suggestions on non-noisy repos

Gate the "Suggested actions to reduce noise" section behind two absolute
floors, AND-ed with the existing relative rules, so it stops firing on
repositories that aren't actually noisy:

- NOISE_MIN_TOTAL (200): suppress the whole section unless the repo has a
  substantial issue volume. Kept above the per-pattern floor so it does
  independent work rather than being subsumed by it.
- NOISE_MIN_PATTERN (100): a pattern must produce enough issues on its own.
  Without it, a long tail of tiny patterns drags the median to ~3, making a
  9-issue pattern look "3x the median" and get flagged as noise.

Also harden the relative rules: the >=10% share rule now only applies with
>=8 distinct patterns (with fewer, an even split already exceeds 10% each),
and the >=3x multiple rule measures against the median (new medianOf) instead
of the mean, so one huge pattern can't inflate the baseline and mask smaller
disproportionate patterns.

Co-Authored-By: Claude <noreply@anthropic.com>

Author: alerizzo

.changeset/tune-issues-overview-noise-suggestions.md

@@ -0,0 +1,16 @@
+---
+"@codacy/codacy-cloud-cli": patch
+---
+
+Stop `issues --overview` from suggesting noise reduction on repositories that aren't
+actually noisy. The "Suggested actions to reduce noise" section now requires two absolute
+floors before anything is suggested: the repository must have at least 200 issues in total,
+and an individual pattern must produce at least 100 issues on its own. The per-pattern floor
+matters because a repository with a long tail of tiny patterns pulls the median issues-per-
+pattern very low, which previously made a pattern with only a handful of issues look
+disproportionate — now a rule has to genuinely flood the repo before it's flagged. On top of
+those floors, a pattern must still show a relative signal: the "dominant share" rule (≥10% of
+all issues) only applies when there are at least 8 distinct patterns (with fewer, an even
+split already exceeds 10% each), and the "disproportionate count" rule now compares each
+pattern against the **median** issues-per-pattern instead of the mean, so a single huge
+pattern can no longer inflate the baseline and hide smaller-but-still-disproportionate ones.

SPECS/README.md

@@ -74,3 +74,4 @@ _No pending tasks._ All commands implemented.
 | 2026-06-24 | `findings` and `finding` now surface the vulnerable dependency's import chain from the new `dependencyChains` field: Direct (`Update <pkg> to <fixed>`) vs Transitive (`<chain> (Fixed in <fixed>)`), with the middle collapsed to `... N more ...` for 4+ packages. List shows the first chain + `... and X more`; detail shows all chains aligned under a single label. New helpers in `utils/formatting.ts` (`formatDependencyChain`, `formatDependencyChainsLine`, `formatDependencyChainsBlock`); `dependencyChains` added to both JSON projections (17 new tests, 390 total) |
 | 2026-06-30 | npm-style "update available" notice via `update-notifier@5`: one-time stderr hint when a newer version is published, gated to `--output table` (suppressed for `json`, when piped, in CI, under `npx`). Non-blocking daily background check; never auto-updates. New `src/version.ts` (single source of name/version) + `src/utils/update-check.ts` (`maybeNotifyUpdate`); `preAction` hook + `--no-update-notifier` flag wired in `index.ts`. Opt-outs: `CODACY_DISABLE_UPDATE_CHECK`, `NO_UPDATE_NOTIFIER`, `--no-update-notifier`. `package.json` `overrides` pin transitive `got@^11.8.6`/`package-json@^7` (CVE-2022-33987) (7 new tests, 409 total) |
 | 2026-07-07 | `ls` and `directories` commands: browse a repository's folders/files with quality metrics (Grade/Issues/Complexity/Duplication/Coverage). Auto-detect provider/org/repo and the cwd-relative path; `--path`/`--branch` options; `directories --plus-children` shows one extra level as a `└─` tree (header adds `, M subdirectories`). `--sort`/`--direction` (server-side; in `ls`, directories and files sorted independently), and `ls --search <term>` (files only; folds the path into the search as `<path>/%<term>` and shows full paths). Duplication uses `numberOfClones`; Complexity uses `complexity` (hotspots). Both fetch **all** pages (no pagination warning) via new `src/utils/repo-tree.ts` (path resolution + `resolveSort`/`resolveDirection` + `fetchAllDirectories`/`fetchAllFiles`). Row markers `▸` folder / dim `·` file (no emojis). Promoted `formatGrade` to `utils/formatting.ts` (now also colors E red) and added `formatCountCell`/`formatCoverageCell` (48 new tests, 457 total) |
+| 2026-07-08 | `issues --overview` noise suggestions tuned to stop firing on low-volume repos: added a `NOISE_MIN_TOTAL` (200) floor on the repo's total issues that suppresses the whole "reduce noise" section below it, and a `NOISE_MIN_PATTERN` (100) absolute floor on each pattern's own count (AND-gated with the relative rules) so a long tail of tiny patterns can't drag the median down and make a ~9-issue pattern look noisy — the total floor is kept above the per-pattern floor so it isn't dead code; the ≥10% share rule now only applies with ≥8 distinct patterns (`NOISE_MIN_PATTERNS_FOR_SHARE`, since with fewer an even split already exceeds 10%); and the ≥3× multiple rule now measures against the **median** (via new `medianOf()`) instead of the mean, so a single huge pattern can no longer inflate the baseline and mask smaller disproportionate patterns (4 new tests, 464 total) |

SPECS/commands/issues.md

@@ -78,11 +78,28 @@ False Positive" (the bucket is keyed on FP probability vs. the configured
 threshold, so at/above threshold = a potential false positive).
 
 After the tables, a **"Suggested actions to reduce noise"** section lists patterns
-worth disabling. A pattern is "noisy" when it accounts for **≥10% of all issues**
-shown, **or** has **≥3× the average** issues-per-pattern. The owning tool is
-resolved by matching the pattern ID against each tool's `prefix` (longest match
-wins); patterns whose tool can't be resolved (no/unknown prefix) are dropped
-silently. The list is capped at 10 with a "… (N more)" note.
+worth disabling. A pattern must clear two absolute floors **and** show a relative
+signal:
+
+- **Total floor** (`NOISE_MIN_TOTAL`, 200): the section is suppressed entirely
+  unless the repo has ≥200 issues in total — on low-volume repos, disabling a rule
+  to shave a handful of issues isn't real noise reduction. Kept above the
+  per-pattern floor so it does independent work (were they equal, any pattern that
+  clears the per-pattern floor would already push the repo past an equal total
+  floor, making it dead code).
+- **Per-pattern floor** (`NOISE_MIN_PATTERN`, 100): the individual pattern must
+  have ≥100 issues on its own. Without it, a long tail of tiny patterns drags the
+  median down (e.g. to 3) so far that a pattern with only ~9 issues clears the
+  relative bar below — yet 9 issues is nothing worth disabling a rule over.
+- **Relative signal** (either one): accounts for **≥10% of all issues** shown
+  (only applied when there are **≥8 distinct patterns**, since with fewer an even
+  split already exceeds 10% each), **or** has **≥3× the median** issues-per-pattern.
+  The median (not the mean) is used so a single huge pattern can't inflate the
+  baseline and mask smaller-but-still-disproportionate patterns.
+
+The owning tool is resolved by matching the pattern ID against each tool's
+`prefix` (longest match wins); patterns whose tool can't be resolved (no/unknown
+prefix) are dropped silently. The list is capped at 10 with a "… (N more)" note.
 
 The suggested step depends on **how the pattern is managed**, since not every
 pattern can be disabled through the CLI:

src/commands/AGENTS.md

@@ -259,7 +259,7 @@ Keeps the two command handlers thin: they only supply the API-specific callbacks
 - **List mode** (default): card-style format sorted by severity (Error > High > Warning > Info)
 - **Overview mode** (`-O, --overview`): seven count tables — Category, Severity, Language, Tag, Pattern, Author, False Positives
   - The False Positives table relabels the API's raw bucket names via `FALSE_POSITIVE_LABELS`: `belowThreshold` → "Not a False Positive", `equalOrAboveThreshold` → "Potential False Positive" (the threshold is on FP probability, so at/above = potential FP — matching `printIssueCard`)
-  - **Noise suggestions**: after the tables, `detectNoisyPatterns()` flags patterns that account for ≥10% of all issues (`NOISE_SHARE`) **or** have ≥3× the average issues-per-pattern (`NOISE_AVG_MULTIPLE`), sorted by count desc. For each, `resolvePatternTool()` maps the pattern ID to its owning tool by matching `Tool.prefix` (e.g. `Bandit_B101` → prefix `Bandit_`; longest match wins) against the global tool list (`fetchAllTools()` / `ToolsService.listTools`). Resolved ones print a `> codacy pattern <tool> <patternId> --disable` line under "Suggested actions to reduce noise". Patterns whose tool can't be resolved (no/unmatched prefix) are **silently discarded**. The tools fetch only happens when noisy patterns exist; JSON output is unaffected (raw counts only)
+  - **Noise suggestions**: after the tables, `detectNoisyPatterns()` flags noisy patterns, sorted by count desc. A pattern must clear **two absolute floors** and show a **relative signal**: (1) the repo must have at least `NOISE_MIN_TOTAL` (200) issues total, else the whole section is suppressed — kept above `NOISE_MIN_PATTERN` so it does independent work (were they equal, any pattern clearing the per-pattern floor would already push the repo past an equal total floor, making it dead code); (2) the individual pattern must have at least `NOISE_MIN_PATTERN` (100) issues — this AND-gate is what stops a long tail of tiny patterns (which drags the median to ~3) from making a 9-issue pattern look "3× the median"; (3) *and* it must either account for ≥`NOISE_SHARE` (10%) of all issues **or** have ≥`NOISE_AVG_MULTIPLE` (3×) the **median** issues-per-pattern. The share rule only applies when there are at least `NOISE_MIN_PATTERNS_FOR_SHARE` (8) distinct patterns — with fewer patterns an even split already exceeds 10% each, so the signal is meaningless. The median (not the mean, via `medianOf()`) is deliberate: a single huge pattern would inflate a mean baseline and mask smaller-but-still-disproportionate patterns. For each noisy pattern, `resolvePatternTool()` maps the pattern ID to its owning tool by matching `Tool.prefix` (e.g. `Bandit_B101` → prefix `Bandit_`; longest match wins) against the global tool list (`fetchAllTools()` / `ToolsService.listTools`). Resolved ones print a `> codacy pattern <tool> <patternId> --disable` line under "Suggested actions to reduce noise". Patterns whose tool can't be resolved (no/unmatched prefix) are **silently discarded**. The tools fetch only happens when noisy patterns exist; JSON output is unaffected (raw counts only)
 - **Filters**: `--branch`, `--patterns`, `--tools`, `--severities`, `--categories`, `--languages`, `--tags`, `--authors`, `--limit`
 - **`--false-positives [value]`** (`-F`): tri-state filter — `true` (default when flag present) sends `onlyPotentialFalsePositives: true`, `false` sends `onlyPotentialFalsePositives: false`, omitted sends nothing
 - **`--ignore` mode** (`-I`): fetches all issues matching current filters (all pages), then calls `AnalysisService.bulkIgnoreIssues` in batches of 100

src/commands/issues.test.ts

@@ -376,8 +376,9 @@ describe("issues command", () => {
     });
 
     it("shows no suggestions and skips the tools fetch when nothing is noisy", async () => {
-      // Twelve evenly-sized patterns: each is ~8.3% of total and equal to the
-      // average, so none crosses the >=10% or >=3x-average thresholds.
+      // Twelve evenly-sized patterns: each is ~8.3% of total (below the >=10%
+      // share floor of 120) and equal to the median (below the >=3x-median floor
+      // of 300), so none crosses either threshold.
       const patterns = Array.from({ length: 12 }, (_, i) => ({
         id: `Tool_${i}`,
         title: `Pattern ${i}`,
@@ -406,6 +407,169 @@ describe("issues command", () => {
       expect(output).not.toContain("Suggested actions to reduce noise");
       expect(ToolsService.listTools).not.toHaveBeenCalled();
     });
+
+    it("makes no suggestions below the absolute total floor", async () => {
+      // A single pattern of 120 that clears the per-pattern floor (100) and is
+      // disproportionate (median 6, 3x = 18; 80% share), so everything except the
+      // total floor would flag it. But the repo has only 150 issues total, below
+      // NOISE_MIN_TOTAL (200) — so the whole section is suppressed regardless.
+      const patterns = [
+        { id: "Bandit_B101", title: "Use of assert detected", total: 120 },
+        ...Array.from({ length: 5 }, (_, i) => ({
+          id: `Other_${i}`,
+          title: `Pattern ${i}`,
+          total: 6,
+        })),
+      ];
+      vi.mocked(AnalysisService.issuesOverview).mockResolvedValue({
+        data: {
+          counts: {
+            categories: [],
+            levels: [{ name: "Warning", total: 150 }],
+            languages: [],
+            tags: [],
+            patterns,
+            authors: [],
+            potentialFalsePositives: [],
+          },
+        },
+      } as any);
+
+      const program = createProgram();
+      await program.parseAsync([
+        "node", "test", "issues", "gh", "test-org", "test-repo", "--overview",
+      ]);
+
+      const output = getAllOutput();
+      expect(output).not.toContain("Suggested actions to reduce noise");
+      // Nothing is noisy, so the tools lookup is skipped entirely.
+      expect(ToolsService.listTools).not.toHaveBeenCalled();
+    });
+
+    it("does not apply the share rule when there are too few patterns", async () => {
+      // Five patterns of comparable size: {120, 80, 80, 80, 80}, total 440.
+      // The 120 is 27% of the total, but with only 5 patterns an even split is
+      // already 20% each, so the share rule is disabled. And 120 < 3x median(80)
+      // = 240, so the multiple rule doesn't fire either → nothing is noisy.
+      const patterns = [
+        { id: "Bandit_B101", title: "Use of assert detected", total: 120 },
+        ...Array.from({ length: 4 }, (_, i) => ({
+          id: `Other_${i}`,
+          title: `Pattern ${i}`,
+          total: 80,
+        })),
+      ];
+      vi.mocked(AnalysisService.issuesOverview).mockResolvedValue({
+        data: {
+          counts: {
+            categories: [],
+            levels: [{ name: "Warning", total: 440 }],
+            languages: [],
+            tags: [],
+            patterns,
+            authors: [],
+            potentialFalsePositives: [],
+          },
+        },
+      } as any);
+
+      const program = createProgram();
+      await program.parseAsync([
+        "node", "test", "issues", "gh", "test-org", "test-repo", "--overview",
+      ]);
+
+      const output = getAllOutput();
+      expect(output).not.toContain("Suggested actions to reduce noise");
+      expect(ToolsService.listTools).not.toHaveBeenCalled();
+    });
+
+    it("flags a secondary pattern a mean baseline would have masked", async () => {
+      // A mega-outlier (5000) drags the *mean* to 512, so the old 3x-mean floor
+      // of 1536 would have hidden the genuinely-disproportionate 120-issue pattern
+      // (24x the typical 5). The median floor (3x median 5 = 15) catches both, and
+      // 120 clears the absolute per-pattern floor of 100.
+      const patterns = [
+        { id: "Bandit_B608", title: "Possible SQL injection", total: 5000 },
+        { id: "Bandit_B101", title: "Use of assert detected", total: 120 },
+        ...Array.from({ length: 8 }, (_, i) => ({
+          id: `Other_${i}`,
+          title: `Pattern ${i}`,
+          total: 5,
+        })),
+      ];
+      vi.mocked(AnalysisService.issuesOverview).mockResolvedValue({
+        data: {
+          counts: {
+            categories: [],
+            levels: [{ name: "Warning", total: 5160 }],
+            languages: [],
+            tags: [],
+            patterns,
+            authors: [],
+            potentialFalsePositives: [],
+          },
+        },
+      } as any);
+      vi.mocked(ToolsService.listTools).mockResolvedValue(banditTool as any);
+      vi.mocked(AnalysisService.listRepositoryTools).mockResolvedValue(
+        banditRepoTool() as any,
+      );
+      vi.mocked(AnalysisService.listRepositoryToolPatterns).mockResolvedValue(
+        banditPattern() as any,
+      );
+
+      const program = createProgram();
+      await program.parseAsync([
+        "node", "test", "issues", "gh", "test-org", "test-repo", "--overview",
+      ]);
+
+      const output = getAllOutput().replace(/\x1b\[[0-9;]*m/g, "");
+      expect(output).toContain("Suggested actions to reduce noise");
+      // The mega-outlier and the secondary pattern are both suggested.
+      expect(output).toContain("codacy pattern Bandit Bandit_B608 --disable");
+      expect(output).toContain("codacy pattern Bandit Bandit_B101 --disable");
+      // The typical 5-issue patterns are not.
+      expect(output).not.toContain('Disable "Pattern 0"');
+    });
+
+    it("does not flag a disproportionate pattern below the per-pattern floor", async () => {
+      // A repo of 210 issues (above NOISE_MIN_TOTAL) where one pattern of 90 is
+      // dominant — 43% share, and well above 3x the median of 8 (24). It clears
+      // every gate except the per-pattern floor: 90 < NOISE_MIN_PATTERN (100). A
+      // rule producing 90 issues isn't a flood worth disabling, so despite being
+      // disproportionate it must not be suggested.
+      const patterns = [
+        { id: "Bandit_B101", title: "Use of assert detected", total: 90 },
+        ...Array.from({ length: 15 }, (_, i) => ({
+          id: `Other_${i}`,
+          title: `Pattern ${i}`,
+          total: 8,
+        })),
+      ];
+      vi.mocked(AnalysisService.issuesOverview).mockResolvedValue({
+        data: {
+          counts: {
+            categories: [],
+            levels: [{ name: "Warning", total: 210 }],
+            languages: [],
+            tags: [],
+            patterns,
+            authors: [],
+            potentialFalsePositives: [],
+          },
+        },
+      } as any);
+
+      const program = createProgram();
+      await program.parseAsync([
+        "node", "test", "issues", "gh", "test-org", "test-repo", "--overview",
+      ]);
+
+      const output = getAllOutput();
+      expect(output).not.toContain("Suggested actions to reduce noise");
+      // Nothing clears the absolute floor, so the tools lookup is skipped.
+      expect(ToolsService.listTools).not.toHaveBeenCalled();
+    });
   });
 
   it("should pass filter options to the API body", async () => {