circle-ir-ai 2.7.1 → 2.7.3

package/CHANGELOG.md

@@ -5,6 +5,71 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [2.7.3] - 2026-05-16
+
+### Fixed
+
+- **#45: `generate-spec`'s interactive conflict prompt leaked to stdout
+  and hung non-TTY runs.** `conflict-resolver.ts:promptUser()` had two
+  issues:
+  1. `readline.createInterface({ output: process.stdout })` — the
+     `Choose option (s/o/r):` text went to stdout, breaking
+     `-f json -q` piping.
+  2. No non-TTY guard — running in CI / `< /dev/null` / a pipe would
+     either hang forever or read garbage.
+
+  Fix: route readline output to `process.stderr`; when
+  `!process.stdin.isTTY`, return `'skip'` immediately so the
+  generator's existing "Spec already exists at ... Use --overwrite"
+  message fires cleanly on stderr.
+
+- **#54: `generate-spec` wrote `.specifica/` to the wrong project
+  root for directory targets.** `findProjectRoot()` always started
+  the marker walk at `path.dirname(path.resolve(filePath))` — which
+  for a directory dropped one level below the user's intent and
+  skipped that directory's own `.git` / `package.json`. In a
+  monorepo this surfaced `outer/.specifica/` instead of
+  `outer/inner-proj/.specifica/`.
+
+  Fix: detect whether `filePath` is a directory via `fs.statSync`
+  and start the walk AT it; only fall back to `dirname` for file
+  targets.
+
+- **#56: `quality` ignored `cognium.config.json` include/exclude
+  globs.** `HealthScoreCalculator` declared `includePatterns` /
+  `excludePatterns` on its options interface but never applied them
+  in `collectFileInfo`'s walk — only hardcoded regex skips
+  (`node_modules`, `.git`, etc.) ran. Users adding excludes to
+  `cognium.config.json` saw no change in reported Files/LOC.
+
+  Fix: applied user globs via `minimatch` (already a dep) inside
+  the walk, alongside the existing built-in skips. Built-in skips
+  remain first for cheap rejection of vendored dirs.
+  `QualityScoreOptions` gained `includePatterns` / `excludePatterns`
+  for pass-through. cognium-ai 2.7.4 wires them to
+  `getEffectiveOptions()`.
+
+## [2.7.2] - 2026-05-08
+
+### Changed
+
+- **circle-ir dep upgraded `^3.20.0` → `^3.21.0`.** Brings positional-
+  argument taint sources for Bash (`$1`–`$9`, `$@`, `$*`, `${1}`,
+  etc.) — closes the highest-priority residual from #33. Verified
+  end-to-end: `eval "echo $1"` and `cat "/etc/app/$2"` now produce
+  CWE-94 / CWE-22 findings on `--no-llm` runs, where 3.20.0 produced
+  zero.
+
+  The release also added detection logic for command substitution
+  (`VAR=$(curl ...)`) and untrusted env vars (`USER_INPUT`, `HTTP_*`,
+  `REQUEST_*`, etc.) but those sources don't yet reach `eval` /
+  code-injection sinks — likely a source-type ↔ sink-type mapping
+  in circle-ir's findings generator (`io_input`/`network_input`/
+  `env_input` not yet wired to `code_injection`). Refined ask
+  posted on #33.
+
+  No circle-ir-ai source changes — pure dep bump. 478 tests pass.
+
 ## [2.7.1] - 2026-05-07
 
 ### Fixed

package/dist/health-score/calculator.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"calculator.d.ts","sourceRoot":"","sources":["../../src/health-score/calculator.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAaH,OAAO,EAAiB,KAAK,UAAU,EAAE,MAAM,6BAA6B,CAAC;AAC7E,OAAO,EAAmB,KAAK,gBAAgB,EAAE,MAAM,2BAA2B,CAAC;AACnF,OAAO,EAAkB,KAAK,cAAc,EAAE,MAAM,0BAA0B,CAAC;AAC/E,OAAO,EAYL,KAAK,YAAY,EAKlB,MAAM,cAAc,CAAC;AAEtB;;GAEG;AACH,MAAM,WAAW,kBAAkB;IACjC,4BAA4B;IAC5B,eAAe,CAAC,EAAE,OAAO,CAAC;IAC1B,0BAA0B;IAC1B,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,iCAAiC;IACjC,eAAe,CAAC,EAAE,OAAO,CAAC;IAC1B,8BAA8B;IAC9B,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,mCAAmC;IACnC,kBAAkB,CAAC,EAAE,OAAO,CAAC;IAC7B,uCAAuC;IACvC,OAAO,CAAC,EAAE,kBAAkB,CAAC;IAC7B,+BAA+B;IAC/B,eAAe,CAAC,EAAE,MAAM,EAAE,CAAC;IAC3B,+BAA+B;IAC/B,eAAe,CAAC,EAAE,MAAM,EAAE,CAAC;IAC3B,wBAAwB;IACxB,UAAU,CAAC,EAAE,CAAC,KAAK,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,KAAK,IAAI,CAAC;IACvD,wCAAwC;IACxC,kBAAkB,CAAC,EAAE,UAAU,CAAC;IAChC,sCAAsC;IACtC,gBAAgB,CAAC,EAAE,gBAAgB,CAAC;IACpC,oCAAoC;IACpC,cAAc,CAAC,EAAE,cAAc,CAAC;IAChC,0CAA0C;IAC1C,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB;AAED;;GAEG;AACH,MAAM,WAAW,kBAAkB;IACjC,QAAQ,EAAE,MAAM,CAAC;IACjB,eAAe,EAAE,MAAM,CAAC;IACxB,OAAO,EAAE,MAAM,CAAC;IAChB,WAAW,EAAE,MAAM,CAAC;CACrB;AAED;;GAEG;AACH,eAAO,MAAM,eAAe,EAAE,kBAK7B,CAAC;AAEF;;GAEG;AACH,MAAM,WAAW,iBAAiB;IAChC,4BAA4B;IAC5B,YAAY,EAAE,MAAM,CAAC;IACrB,oBAAoB;IACpB,YAAY,EAAE,MAAM,CAAC;IACrB,wBAAwB;IACxB,KAAK,EAAE,OAAO,GAAG,QAAQ,GAAG,QAAQ,GAAG,KAAK,CAAC;IAC7C,kCAAkC;IAClC,UAAU,EAAE;QACV,QAAQ,EAAE,YAAY,CAAC;QACvB,eAAe,EAAE,YAAY,CAAC;QAC9B,OAAO,EAAE,YAAY,CAAC;QACtB,WAAW,EAAE,YAAY,CAAC;KAC3B,CAAC;IACF,mBAAmB;IACnB,OAAO,EAAE,kBAAkB,CAAC;IAC5B,4BAA4B;IAC5B,SAAS,EAAE,MAAM,EAAE,CAAC;IACpB,sBAAsB;IACtB,eAAe,EAAE,MAAM,EAAE,CAAC;IAC1B,oBAAoB;IACpB,IAAI,EAAE;QACJ,SAAS,EAAE,MAAM,CAAC;QAClB,aAAa,EAAE,MAAM,CAAC;QACtB,QAAQ,EAAE,MAAM,CAAC;QACjB,SAAS,EAAE,MAAM,CAAC;QAClB,UAAU,EAAE,MAAM,CAAC;KACpB,CAAC;CACH;AAED;;GAEG;AACH,qBAAa,qBAAqB;IAChC,OAAO,CAAC,OAAO,CAAqB;IACpC,OAAO,CAAC,OAAO,CAAqB;gBAExB,OAAO,GAAE,kBAAuB;IAkB5C;;OAEG;IACG,SAAS,CAAC,SAAS,EAAE,MAAM,GAAG,OAAO,CAAC,iBAAiB,CAAC;IAoJ9D;;OAEG;YACW,eAAe;IAwO7B;;;OAGG;IACH,OAAO,CAAC,mBAAmB;IA8D3B;;OAEG;IACH,OAAO,CAAC,uBAAuB;CAiEhC;AA4BD;;GAEG;AACH,wBAAsB,oBAAoB,CACxC,SAAS,EAAE,MAAM,EACjB,OAAO,GAAE,kBAAuB,GAC/B,OAAO,CAAC,iBAAiB,CAAC,CAG5B;AAED;;GAEG;AACH,wBAAsB,gBAAgB,CAAC,SAAS,EAAE,MAAM,GAAG,OAAO,CAAC,iBAAiB,CAAC,CAOpF;AAED;;GAEG;AACH,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,iBAAiB,GAAG,MAAM,CAgGpE"}

package/dist/health-score/calculator.js

@@ -6,6 +6,7 @@
  */
 import * as fs from 'fs';
 import * as path from 'path';
+import { minimatch } from 'minimatch';
 import { isAnalyzerInitialized, analyze, } from 'circle-ir';
 import { ensureAnalyzerInitialized } from '../utils/analyzer-init.js';
 import { scanDirectory } from '../security-scan/scanner.js';
@@ -210,6 +211,13 @@ export class HealthScoreCalculator {
             /\.min\./,
             /vendor/,
         ];
+        // #56: user-provided include/exclude globs from cognium.config.json
+        // (or CLI flags). HealthScoreOptions has declared these forever but
+        // the walk never applied them — only the hardcoded regex excludes
+        // ran. Result: `quality` reported the same Files/LOC regardless of
+        // user `exclude` entries.
+        const userIncludeGlobs = this.options.includePatterns ?? [];
+        const userExcludeGlobs = this.options.excludePatterns ?? [];
         // Extensions that circle-ir can analyze
         const analyzerExtensions = {
             '.ts': 'typescript',
@@ -239,6 +247,10 @@ export class HealthScoreCalculator {
                     const relativePath = path.relative(directory, fullPath);
                     if (excludePatterns.some((p) => p.test(relativePath)))
                         continue;
+                    // #56: apply user exclude globs (built-in regex skips run first
+                    // to keep the hot path cheap on node_modules / .git).
+                    if (userExcludeGlobs.length && userExcludeGlobs.some((g) => minimatch(relativePath, g, { dot: true })))
+                        continue;
                     if (entry.isDirectory()) {
                         walk(fullPath);
                     }
@@ -246,6 +258,9 @@ export class HealthScoreCalculator {
                         const ext = path.extname(entry.name).toLowerCase();
                         if (!sourceExtensions.includes(ext))
                             continue;
+                        // #56: apply user include globs (if any). Empty = include all.
+                        if (userIncludeGlobs.length && !userIncludeGlobs.some((g) => minimatch(relativePath, g, { dot: true })))
+                            continue;
                         const isTest = testPatterns.some((p) => p.test(entry.name));
                         files.push({ fullPath, relativePath, ext, isTest });
                     }

package/dist/health-score/calculator.js.map

@@ -1 +1 @@
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package/dist/quality/calculator.d.ts

@@ -17,6 +17,10 @@ export declare const DEFAULT_QUALITY_WEIGHTS: QualityWeights;
 export interface QualityScoreOptions {
     weights?: Partial<QualityWeights>;
     onProgress?: (phase: string, progress: number) => void;
+    /** #56: user include globs from cognium.config.json / CLI flags. */
+    includePatterns?: string[];
+    /** #56: user exclude globs from cognium.config.json / CLI flags. */
+    excludePatterns?: string[];
 }
 /**
  * Calculate a quality score for a directory.

package/dist/quality/calculator.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"calculator.d.ts","sourceRoot":"","sources":["../../src/quality/calculator.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAMH,OAAO,KAAK,EAAE,kBAAkB,EAAqC,MAAM,YAAY,CAAC;AAOxF,MAAM,WAAW,cAAc;IAC7B,cAAc,EAAE,MAAM,CAAC;IACvB,YAAY,EAAE,MAAM,CAAC;IACrB,qBAAqB,EAAE,MAAM,CAAC;IAC9B,oBAAoB,EAAE,MAAM,CAAC;IAC7B,mBAAmB,EAAE,MAAM,CAAC;CAC7B;AAED,eAAO,MAAM,uBAAuB,EAAE,cAMrC,CAAC;AAMF,MAAM,WAAW,mBAAmB;IAClC,OAAO,CAAC,EAAE,OAAO,CAAC,cAAc,CAAC,CAAC;IAClC,UAAU,CAAC,EAAE,CAAC,KAAK,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,KAAK,IAAI,CAAC;CACxD;AAkTD;;;;;GAKG;AACH,wBAAsB,qBAAqB,CACzC,SAAS,EAAE,MAAM,EACjB,OAAO,GAAE,mBAAwB,GAChC,OAAO,CAAC,kBAAkB,CAAC,CAwE7B;AAMD;;GAEG;AACH,wBAAgB,mBAAmB,CAAC,MAAM,EAAE,kBAAkB,GAAG,MAAM,CAqDtE"}
+{"version":3,"file":"calculator.d.ts","sourceRoot":"","sources":["../../src/quality/calculator.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAMH,OAAO,KAAK,EAAE,kBAAkB,EAAqC,MAAM,YAAY,CAAC;AAOxF,MAAM,WAAW,cAAc;IAC7B,cAAc,EAAE,MAAM,CAAC;IACvB,YAAY,EAAE,MAAM,CAAC;IACrB,qBAAqB,EAAE,MAAM,CAAC;IAC9B,oBAAoB,EAAE,MAAM,CAAC;IAC7B,mBAAmB,EAAE,MAAM,CAAC;CAC7B;AAED,eAAO,MAAM,uBAAuB,EAAE,cAMrC,CAAC;AAMF,MAAM,WAAW,mBAAmB;IAClC,OAAO,CAAC,EAAE,OAAO,CAAC,cAAc,CAAC,CAAC;IAClC,UAAU,CAAC,EAAE,CAAC,KAAK,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,KAAK,IAAI,CAAC;IACvD,oEAAoE;IACpE,eAAe,CAAC,EAAE,MAAM,EAAE,CAAC;IAC3B,oEAAoE;IACpE,eAAe,CAAC,EAAE,MAAM,EAAE,CAAC;CAC5B;AAkTD;;;;;GAKG;AACH,wBAAsB,qBAAqB,CACzC,SAAS,EAAE,MAAM,EACjB,OAAO,GAAE,mBAAwB,GAChC,OAAO,CAAC,kBAAkB,CAAC,CA4E7B;AAMD;;GAEG;AACH,wBAAgB,mBAAmB,CAAC,MAAM,EAAE,kBAAkB,GAAG,MAAM,CAqDtE"}

package/dist/quality/calculator.js

@@ -307,6 +307,10 @@ export async function calculateQualityScore(directory, options = {}) {
         onProgress: (phase, progress) => {
             options.onProgress?.(phase, progress * 0.8); // 0-80% for health-score
         },
+        // #56: pass user globs through so the file walk honors
+        // cognium.config.json include/exclude.
+        includePatterns: options.includePatterns,
+        excludePatterns: options.excludePatterns,
     });
     const healthResult = await healthCalc.calculate(directory);
     // Phase 2: Map health dimensions to quality passes

package/dist/quality/calculator.js.map

@@ -1 +1 @@
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package/dist/specifica/conflict-resolver.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"conflict-resolver.d.ts","sourceRoot":"","sources":["../../src/specifica/conflict-resolver.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAKH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAErD;;GAEG;AACH,wBAAsB,eAAe,CACnC,QAAQ,EAAE,MAAM,EAChB,UAAU,EAAE,kBAAkB,GAC7B,OAAO,CAAC,MAAM,GAAG,WAAW,GAAG,OAAO,GAAG,QAAQ,CAAC,CA0BpD;AAiFD;;GAEG;AACH,wBAAgB,UAAU,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAEpD;AAED;;GAEG;AACH,wBAAgB,mBAAmB,CAAC,KAAK,EAAE;IACzC,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB,GAAG,kBAAkB,CAiBrB"}
+{"version":3,"file":"conflict-resolver.d.ts","sourceRoot":"","sources":["../../src/specifica/conflict-resolver.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAKH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAErD;;GAEG;AACH,wBAAsB,eAAe,CACnC,QAAQ,EAAE,MAAM,EAChB,UAAU,EAAE,kBAAkB,GAC7B,OAAO,CAAC,MAAM,GAAG,WAAW,GAAG,OAAO,GAAG,QAAQ,CAAC,CA0BpD;AA8FD;;GAEG;AACH,wBAAgB,UAAU,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAEpD;AAED;;GAEG;AACH,wBAAgB,mBAAmB,CAAC,KAAK,EAAE;IACzC,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB,GAAG,kBAAkB,CAiBrB"}

package/dist/specifica/conflict-resolver.js

@@ -35,9 +35,21 @@ export async function resolveConflict(filePath, resolution) {
  * Prompt user for conflict resolution
  */
 async function promptUser(filePath) {
+    // #45: non-interactive guard. When stdin is not a TTY (piped, CI,
+    // redirected), prompting would either hang forever or read garbage —
+    // and worse, with `-f json -q` users get the readline question text
+    // contaminating their stdout JSON. Default to 'skip' silently so
+    // generator.ts's existing "Spec already exists at ... Use --overwrite"
+    // error fires cleanly on stderr.
+    if (!process.stdin.isTTY) {
+        return 'skip';
+    }
+    // #45: readline output to stderr (was stdout) — even when a TTY user
+    // intentionally pipes stdout for the JSON result, the prompt remains
+    // visible on the terminal.
     const rl = readline.createInterface({
         input: process.stdin,
-        output: process.stdout,
+        output: process.stderr,
     });
     return new Promise((resolve) => {
         console.error(`\nFile already exists: ${filePath}`);

package/dist/specifica/conflict-resolver.js.map

@@ -1 +1 @@
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+{"version":3,"file":"conflict-resolver.js","sourceRoot":"","sources":["../../src/specifica/conflict-resolver.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAAE,MAAM,IAAI,CAAC;AACzB,OAAO,KAAK,IAAI,MAAM,MAAM,CAAC;AAC7B,OAAO,KAAK,QAAQ,MAAM,UAAU,CAAC;AAGrC;;GAEG;AACH,MAAM,CAAC,KAAK,UAAU,eAAe,CACnC,QAAgB,EAChB,UAA8B;IAE9B,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,GAAG,UAAU,CAAC;IAExC,QAAQ,QAAQ,EAAE,CAAC;QACjB,KAAK,MAAM;YACT,OAAO,MAAM,CAAC;QAEhB,KAAK,WAAW;YACd,IAAI,MAAM,EAAE,CAAC;gBACX,MAAM,UAAU,CAAC,QAAQ,CAAC,CAAC;YAC7B,CAAC;YACD,OAAO,WAAW,CAAC;QAErB,KAAK,OAAO;YACV,wCAAwC;YACxC,OAAO,CAAC,IAAI,CAAC,4DAA4D,CAAC,CAAC;YAC3E,OAAO,MAAM,UAAU,CAAC,QAAQ,CAAC,CAAC;QAEpC,KAAK,QAAQ;YACX,MAAM,cAAc,CAAC,QAAQ,CAAC,CAAC;YAC/B,OAAO,QAAQ,CAAC;QAElB,KAAK,QAAQ,CAAC;QACd;YACE,OAAO,MAAM,UAAU,CAAC,QAAQ,CAAC,CAAC;IACtC,CAAC;AACH,CAAC;AAED;;GAEG;AACH,KAAK,UAAU,UAAU,CAAC,QAAgB;IACxC,kEAAkE;IAClE,qEAAqE;IACrE,oEAAoE;IACpE,iEAAiE;IACjE,uEAAuE;IACvE,iCAAiC;IACjC,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,KAAK,EAAE,CAAC;QACzB,OAAO,MAAM,CAAC;IAChB,CAAC;IAED,qEAAqE;IACrE,qEAAqE;IACrE,2BAA2B;IAC3B,MAAM,EAAE,GAAG,QAAQ,CAAC,eAAe,CAAC;QAClC,KAAK,EAAE,OAAO,CAAC,KAAK;QACpB,MAAM,EAAE,OAAO,CAAC,MAAM;KACvB,CAAC,CAAC;IAEH,OAAO,IAAI,OAAO,CAAC,CAAC,OAAO,EAAE,EAAE;QAC7B,OAAO,CAAC,KAAK,CAAC,0BAA0B,QAAQ,EAAE,CAAC,CAAC;QACpD,OAAO,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC;QAC1B,OAAO,CAAC,KAAK,CAAC,iCAAiC,CAAC,CAAC;QACjD,OAAO,CAAC,KAAK,CAAC,6DAA6D,CAAC,CAAC;QAC7E,OAAO,CAAC,KAAK,CAAC,oDAAoD,CAAC,CAAC;QACpE,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QAElB,EAAE,CAAC,QAAQ,CAAC,yBAAyB,EAAE,CAAC,MAAM,EAAE,EAAE;YAChD,EAAE,CAAC,KAAK,EAAE,CAAC;YAEX,MAAM,MAAM,GAAG,MAAM,CAAC,WAAW,EAAE,CAAC,IAAI,EAAE,CAAC;YAE3C,QAAQ,MAAM,EAAE,CAAC;gBACf,KAAK,GAAG,CAAC;gBACT,KAAK,WAAW;oBACd,0BAA0B;oBAC1B,UAAU,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,GAAG,EAAE,CAAC,OAAO,CAAC,WAAW,CAAC,CAAC,CAAC;oBACtD,MAAM;gBAER,KAAK,GAAG,CAAC;gBACT,KAAK,QAAQ;oBACX,cAAc,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,GAAG,EAAE,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC;oBACvD,MAAM;gBAER,KAAK,GAAG,CAAC;gBACT,KAAK,MAAM,CAAC;gBACZ;oBACE,OAAO,CAAC,MAAM,CAAC,CAAC;oBAChB,MAAM;YACV,CAAC;QACH,CAAC,CAAC,CAAC;IACL,CAAC,CAAC,CAAC;AACL,CAAC;AAED;;GAEG;AACH,KAAK,UAAU,UAAU,CAAC,QAAgB;IACxC,MAAM,SAAS,GAAG,IAAI,IAAI,EAAE,CAAC,WAAW,EAAE,CAAC,OAAO,CAAC,OAAO,EAAE,GAAG,CAAC,CAAC;IACjE,MAAM,UAAU,GAAG,GAAG,QAAQ,WAAW,SAAS,EAAE,CAAC;IAErD,IAAI,CAAC;QACH,EAAE,CAAC,YAAY,CAAC,QAAQ,EAAE,UAAU,CAAC,CAAC;QACtC,OAAO,CAAC,KAAK,CAAC,qBAAqB,UAAU,EAAE,CAAC,CAAC;IACnD,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,OAAO,CAAC,KAAK,CAAC,4BAA4B,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QACpG,MAAM,KAAK,CAAC;IACd,CAAC;AACH,CAAC;AAED;;GAEG;AACH,KAAK,UAAU,cAAc,CAAC,QAAgB;IAC5C,MAAM,SAAS,GAAG,IAAI,IAAI,EAAE,CAAC,WAAW,EAAE,CAAC,OAAO,CAAC,OAAO,EAAE,GAAG,CAAC,CAAC;IACjE,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC;IACnC,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC;IACnC,MAAM,IAAI,GAAG,IAAI,CAAC,QAAQ,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAC;IAC1C,MAAM,UAAU,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,GAAG,IAAI,IAAI,SAAS,GAAG,GAAG,EAAE,CAAC,CAAC;IAEhE,IAAI,CAAC;QACH,EAAE,CAAC,UAAU,CAAC,QAAQ,EAAE,UAAU,CAAC,CAAC;QACpC,OAAO,CAAC,KAAK,CAAC,4BAA4B,UAAU,EAAE,CAAC,CAAC;IAC1D,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,OAAO,CAAC,KAAK,CAAC,0BAA0B,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QAClG,MAAM,KAAK,CAAC;IACd,CAAC;AACH,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,UAAU,CAAC,QAAgB;IACzC,OAAO,EAAE,CAAC,UAAU,CAAC,QAAQ,CAAC,CAAC;AACjC,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,mBAAmB,CAAC,KAInC;IACC,IAAI,KAAK,CAAC,IAAI,EAAE,CAAC;QACf,OAAO,EAAE,QAAQ,EAAE,MAAM,EAAE,CAAC;IAC9B,CAAC;IAED,IAAI,KAAK,CAAC,SAAS,EAAE,CAAC;QACpB,OAAO;YACL,QAAQ,EAAE,WAAW;YACrB,MAAM,EAAE,KAAK,CAAC,MAAM,KAAK,KAAK,EAAE,oBAAoB;SACrD,CAAC;IACJ,CAAC;IAED,uBAAuB;IACvB,OAAO;QACL,QAAQ,EAAE,QAAQ;QAClB,MAAM,EAAE,IAAI;KACb,CAAC;AACJ,CAAC"}

package/dist/specifica/generator.js

@@ -319,9 +319,25 @@ export async function generateSpecificaForDirectory(dirPath, options = {}) {
 }
 /**
  * Find project root (directory containing package.json, pom.xml, etc.)
+ *
+ * #54: when `filePath` is a directory, the marker walk must start AT that
+ * directory — not one level above. Previously this always did
+ * `path.dirname(...)`, which for a directory target dropped one level
+ * below the user's intent. In a monorepo like
+ *   cognium-test-bench/repos/javascript/cli/.git
+ * the walk skipped `cli`'s own `.git` and landed on
+ * `cognium-test-bench/.git`, writing `.specifica/` to the wrong root.
  */
 function findProjectRoot(filePath) {
-    let current = path.dirname(path.resolve(filePath));
+    const resolved = path.resolve(filePath);
+    let isDirectory = false;
+    try {
+        isDirectory = fs.statSync(resolved).isDirectory();
+    }
+    catch {
+        // Path doesn't exist; fall back to dirname semantics
+    }
+    let current = isDirectory ? resolved : path.dirname(resolved);
     while (current !== '/') {
         // Check for project markers
         const markers = ['package.json', 'pom.xml', 'Cargo.toml', 'pyproject.toml', '.git'];
@@ -336,8 +352,8 @@ function findProjectRoot(filePath) {
             break; // Reached root
         current = parent;
     }
-    // Fallback: use file's directory
-    return path.dirname(path.resolve(filePath));
+    // Fallback: use the directory itself (if target was a dir) or its parent
+    return isDirectory ? resolved : path.dirname(resolved);
 }
 /**
  * Detect language from file extension

package/dist/specifica/generator.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "circle-ir-ai",
-  "version": "2.7.1",
+  "version": "2.7.3",
   "description": "LLM-enhanced SAST analysis built on circle-ir",
   "main": "dist/index.js",
   "module": "dist/index.js",
@@ -92,7 +92,7 @@
   "dependencies": {
     "@ax-llm/ax": "^20.0.0",
     "@mastra/core": "^1.18.0",
-    "circle-ir": "^3.20.0",
+    "circle-ir": "^3.21.0",
     "minimatch": "^10.2.5",
     "p-queue": "^9.1.0"
   },

package/dist/cli/args.d.ts

@@ -1,86 +0,0 @@
-/**
- * CLI Argument Parser
- */
-export type OutputFormat = 'json' | 'summary' | 'sarif' | 'markdown' | 'csv';
-export type Command = 'analyze' | 'benchmark' | 'scan' | 'health' | 'secrets' | 'dead-code' | 'generate-spec' | 'analyze-skill' | 'metrics' | 'trust' | 'compare' | 'quality' | 'understand' | 'spec-diff' | 'cluster';
-export type LogLevel = 'trace' | 'debug' | 'info' | 'warn' | 'error' | 'silent';
-export type BundleType = 'jr-dev' | 'sr-dev' | 'architect' | 'security-review' | 'full-review';
-export interface CliArgs {
-    command: Command;
-    file: string | null;
-    directory: string | null;
-    format: OutputFormat;
-    output: string | null;
-    config: string | null;
-    include: string[];
-    exclude: string[];
-    exitCode: boolean;
-    quiet: boolean;
-    help: boolean;
-    version: boolean;
-    logLevel: LogLevel | null;
-    discoverPatterns: boolean;
-    patternThreshold: number;
-    noLlm: boolean;
-    llmEnrich: boolean;
-    llmVerify: boolean;
-    llmBaseUrl: string | null;
-    llmApiKey: string | null;
-    llmModel: string | null;
-    language: string | null;
-    threads: number;
-    bundle: BundleType | null;
-    expectedResults: string | null;
-    limit: number | null;
-    categories: string[];
-    parallel: number | null;
-    cache: boolean;
-    cacheDir: string | null;
-    clearCache: boolean;
-    streamOutput: string | null;
-    memoryEfficient: boolean;
-    specModel: string | null;
-    specOverwrite: boolean;
-    specSkip: boolean;
-    specNoBackup: boolean;
-    specDesign: boolean;
-    specPrinciples: boolean;
-    specTasks: boolean;
-    specDesignLLM: boolean;
-    specPrinciplesLLM: boolean;
-    specTasksLLM: boolean;
-    specDir: string | null;
-    crossArtifact?: boolean;
-    verification?: boolean;
-    minConfidence?: number;
-    minSeverity?: 'critical' | 'high' | 'medium' | 'low' | 'info';
-    severity: 'critical' | 'high' | 'medium' | 'low' | null;
-    excludeTests: boolean;
-    llmDiscovery: boolean;
-    disablePass: string[];
-    fileTimeout: number;
-    maxFiles: number | null;
-    pathB: string | null;
-    history: boolean;
-    maxCommits: number;
-    includeCategory: string[];
-    excludeCategory: string[];
-    includeTests: boolean;
-    publicAsEntry: boolean;
-    top: number | null;
-    full: boolean;
-    metricCategory: string[];
-    role: string[];
-    securityOnly: boolean;
-    healthSecurity: boolean;
-    healthSecrets: boolean;
-    healthDeadCode: boolean;
-    healthQuality: boolean;
-    healthPerformance: boolean;
-    threshold: number;
-}
-/**
- * Parse command-line arguments.
- */
-export declare function parseArgs(argv: string[]): CliArgs;
-//# sourceMappingURL=args.d.ts.map

package/dist/cli/args.d.ts.map

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