feat: Implement latest PR version filtering for CodeAnalysis issues in services

Author: rostilos

java-ecosystem/libs/core/src/main/java/org/rostilos/codecrow/core/persistence/repository/codeanalysis/CodeAnalysisIssueRepository.java

@@ -107,6 +107,42 @@ List<CodeAnalysisIssue> findByProjectIdAndPrNumberAndFilePath(
             @Param("prNumber") Long prNumber,
             @Param("filePath") String filePath);
 
+    /**
+     * Find issues for the <b>latest PR version only</b>.
+     * Scopes to the analysis with MAX(prVersion) for this PR number.
+     * Used by the PR source code viewer (file tree counts).
+     */
+    @Query("SELECT cai FROM CodeAnalysisIssue cai " +
+            "WHERE cai.analysis.project.id = :projectId " +
+            "AND cai.analysis.prNumber = :prNumber " +
+            "AND cai.analysis.prVersion = (" +
+            "  SELECT MAX(a.prVersion) FROM CodeAnalysis a " +
+            "  WHERE a.project.id = :projectId AND a.prNumber = :prNumber" +
+            ") " +
+            "ORDER BY cai.filePath ASC, cai.lineNumber ASC")
+    List<CodeAnalysisIssue> findByProjectIdAndPrNumberLatestVersion(
+            @Param("projectId") Long projectId,
+            @Param("prNumber") Long prNumber);
+
+    /**
+     * Find issues for a specific file in the <b>latest PR version only</b>.
+     * Scopes to the analysis with MAX(prVersion) for this PR number.
+     * Used by the PR source code viewer (inline issue annotations).
+     */
+    @Query("SELECT cai FROM CodeAnalysisIssue cai " +
+            "WHERE cai.analysis.project.id = :projectId " +
+            "AND cai.analysis.prNumber = :prNumber " +
+            "AND cai.filePath = :filePath " +
+            "AND cai.analysis.prVersion = (" +
+            "  SELECT MAX(a.prVersion) FROM CodeAnalysis a " +
+            "  WHERE a.project.id = :projectId AND a.prNumber = :prNumber" +
+            ") " +
+            "ORDER BY cai.lineNumber ASC")
+    List<CodeAnalysisIssue> findByProjectIdAndPrNumberAndFilePathLatestVersion(
+            @Param("projectId") Long projectId,
+            @Param("prNumber") Long prNumber,
+            @Param("filePath") String filePath);
+
     // ── Aggregate queries (for analytics — avoid loading full entity graphs) ──
 
     @Query("SELECT COUNT(cai) FROM CodeAnalysisIssue cai " +

java-ecosystem/libs/core/src/main/java/org/rostilos/codecrow/core/service/CodeAnalysisService.java

@@ -930,6 +930,22 @@ public List<CodeAnalysisIssue> findIssuesByPrNumberAndFilePath(Long projectId, L
                 issueRepository.findByProjectIdAndPrNumberAndFilePath(projectId, prNumber, filePath));
     }
 
+    /**
+     * Find all issues for the <b>latest PR version only</b>.
+     * No cross-iteration deduplication needed — single iteration scope.
+     */
+    public List<CodeAnalysisIssue> findIssuesByPrNumberLatestVersion(Long projectId, Long prNumber) {
+        return issueRepository.findByProjectIdAndPrNumberLatestVersion(projectId, prNumber);
+    }
+
+    /**
+     * Find issues for a specific file in the <b>latest PR version only</b>.
+     * No cross-iteration deduplication needed — single iteration scope.
+     */
+    public List<CodeAnalysisIssue> findIssuesByPrNumberAndFilePathLatestVersion(Long projectId, Long prNumber, String filePath) {
+        return issueRepository.findByProjectIdAndPrNumberAndFilePathLatestVersion(projectId, prNumber, filePath);
+    }
+
     /**
      * Deduplicate issues that span multiple analyses on the same branch.
      * When the same logical issue is tracked across analyses (via trackedFromIssueId),
@@ -987,24 +1003,7 @@ private List<CodeAnalysisIssue> deduplicateBranchIssues(List<CodeAnalysisIssue>
             }
         }
 
-        // Pass 3: safety-net dedup for issues that survived with null fingerprints.
-        // Group by (normalizedTitle + lineNumber) and keep only the latest version.
-        Map<String, CodeAnalysisIssue> byTitleLine = new LinkedHashMap<>();
-        for (CodeAnalysisIssue issue : byContentFp.values()) {
-            String title = issue.getTitle();
-            int line = issue.getLineNumber() != null ? issue.getLineNumber() : 0;
-            if (title != null && !title.isBlank()) {
-                String key = IssueFingerprint.normalizeTitle(title) + "::" + line;
-                CodeAnalysisIssue existing = byTitleLine.get(key);
-                if (existing == null || issue.getAnalysis().getId() > existing.getAnalysis().getId()) {
-                    byTitleLine.put(key, issue);
-                }
-            } else {
-                byTitleLine.put("_id_" + issue.getId(), issue);
-            }
-        }
-
-        return new ArrayList<>(byTitleLine.values());
+        return new ArrayList<>(byContentFp.values());
     }
 
     public void markIssueAsResolved(Long issueId) {

java-ecosystem/services/web-server/src/main/java/org/rostilos/codecrow/webserver/analysis/service/FileViewService.java

@@ -362,8 +362,8 @@ public Optional<AnalysisFilesResponse> listPrFiles(Long projectId, Long prNumber
             return Optional.empty();
         }
 
-        // Aggregate issues across all analyses for this PR number
-        List<CodeAnalysisIssue> issues = codeAnalysisService.findIssuesByPrNumber(projectId, prNumber);
+        // Only show issues from the latest PR version (not accumulated across all iterations)
+        List<CodeAnalysisIssue> issues = codeAnalysisService.findIssuesByPrNumberLatestVersion(projectId, prNumber);
         Map<String, List<CodeAnalysisIssue>> issuesByFile = issues.stream()
                 .filter(i -> i.getFilePath() != null)
                 .filter(FileViewService::hasTitle)
@@ -416,8 +416,8 @@ public Optional<FileViewResponse> getPrFileView(Long projectId, Long prNumber, S
         int lineCount = countLines(content);
         LineHashSequence lineHashes = LineHashSequence.from(content);
 
-        // Aggregate issues across all analyses for this PR number
-        List<CodeAnalysisIssue> fileIssues = codeAnalysisService.findIssuesByPrNumberAndFilePath(projectId, prNumber, filePath);
+        // Only show issues from the latest PR version (not accumulated across all iterations)
+        List<CodeAnalysisIssue> fileIssues = codeAnalysisService.findIssuesByPrNumberAndFilePathLatestVersion(projectId, prNumber, filePath);
         List<FileViewResponse.InlineIssue> inlineIssues = fileIssues.stream()
                 .filter(FileViewService::hasTitle)
                 .filter(i -> !i.isResolved())
@@ -477,8 +477,8 @@ public Optional<FileSnippetResponse> getPrFileSnippet(
             snippetLines.add(new FileSnippetResponse.SnippetLine(i, lineContent));
         }
 
-        // Get issues for this PR and file, filtered to the snippet range
-        List<CodeAnalysisIssue> allIssues = codeAnalysisService.findIssuesByPrNumberAndFilePath(projectId, prNumber, filePath);
+        // Only show issues from the latest PR version, filtered to the snippet range
+        List<CodeAnalysisIssue> allIssues = codeAnalysisService.findIssuesByPrNumberAndFilePathLatestVersion(projectId, prNumber, filePath);
         int finalStartLine = startLine;
         int finalEndLine = endLine;
         List<FileViewResponse.InlineIssue> inlineIssues = allIssues.stream()
@@ -543,7 +543,8 @@ public Optional<FileSnippetResponse> getPrFileSnippetByRange(
             snippetLines.add(new FileSnippetResponse.SnippetLine(i, lineContent));
         }
 
-        List<CodeAnalysisIssue> allIssues = codeAnalysisService.findIssuesByPrNumberAndFilePath(projectId, prNumber, filePath);
+        // Only show issues from the latest PR version, filtered to the line range
+        List<CodeAnalysisIssue> allIssues = codeAnalysisService.findIssuesByPrNumberAndFilePathLatestVersion(projectId, prNumber, filePath);
         int finalStart = startLine;
         int finalEnd = endLine;
         List<FileViewResponse.InlineIssue> inlineIssues = allIssues.stream()