Merge pull request #41 from rostilos/rag-pipeline-memory-leak-at-inde…

java-ecosystem/libs/analysis-engine/src/main/java/org/rostilos/codecrow/analysisengine/dto/request/ai/AiRequestPreviousIssueDTO.java

@@ -7,14 +7,15 @@ public record AiRequestPreviousIssueDTO(
         String id,
         String type, // security|quality|performance|style
         String severity, // critical|high|medium|low|info
-        String title,
+        String reason,
         String suggestedFixDescription,
+        String suggestedFixDiff,
         String file,
         Integer line,
         String branch,
         String pullRequestId,
         String status, // open|resolved|ignored
-        String issueCategory
+        String category
 ) {
     public static AiRequestPreviousIssueDTO fromEntity(CodeAnalysisIssue issue) {
         String categoryStr = issue.getIssueCategory() != null 
@@ -23,9 +24,10 @@ public static AiRequestPreviousIssueDTO fromEntity(CodeAnalysisIssue issue) {
         return new AiRequestPreviousIssueDTO(
                 String.valueOf(issue.getId()),
                 categoryStr,
-                issue.getSeverity() != null ? issue.getSeverity().name().toLowerCase() : null,
+                issue.getSeverity() != null ? issue.getSeverity().name() : null,
                 issue.getReason(),
                 issue.getSuggestedFixDescription(),
+                issue.getSuggestedFixDiff(),
                 issue.getFilePath(),
                 issue.getLineNumber(),
                 issue.getAnalysis() == null ? null : issue.getAnalysis().getBranchName(),

java-ecosystem/libs/analysis-engine/src/main/java/org/rostilos/codecrow/analysisengine/processor/analysis/BranchAnalysisProcessor.java

@@ -372,15 +372,15 @@ private void mapCodeAnalysisIssuesToBranch(Set<String> changedFiles, Branch bran
                 if (existing.isPresent()) {
                     bc = existing.get();
                     bc.setSeverity(issue.getSeverity());
-                    branchIssueRepository.save(bc);
+                    branchIssueRepository.saveAndFlush(bc);
                 } else {
                     bc = new BranchIssue();
                     bc.setBranch(branch);
                     bc.setCodeAnalysisIssue(issue);
                     bc.setResolved(issue.isResolved());
                     bc.setSeverity(issue.getSeverity());
                     bc.setFirstDetectedPrNumber(issue.getAnalysis() != null ? issue.getAnalysis().getPrNumber() : null);
-                    branchIssueRepository.save(bc);
+                    branchIssueRepository.saveAndFlush(bc);
                 }
             }
         }

java-ecosystem/libs/core/src/main/resources/db/migration/1.1.0/V1.1.0__add_info_severity_to_constraint.sql

@@ -0,0 +1,9 @@
+-- Add INFO to the severity check constraint on code_analysis_issue table
+-- This is needed because INFO was added to IssueSeverity enum but the constraint wasn't updated
+
+-- Drop the existing constraint and recreate with INFO included
+ALTER TABLE code_analysis_issue DROP CONSTRAINT IF EXISTS code_analysis_issue_severity_check;
+
+ALTER TABLE code_analysis_issue 
+ADD CONSTRAINT code_analysis_issue_severity_check 
+CHECK (severity IN ('HIGH', 'MEDIUM', 'LOW', 'INFO', 'RESOLVED'));

java-ecosystem/libs/vcs-client/src/main/java/org/rostilos/codecrow/vcsclient/bitbucket/cloud/actions/CommentOnBitbucketCloudAction.java

@@ -33,6 +33,15 @@ public CommentOnBitbucketCloudAction(
     }
 
     public void postSummaryResult(String textContent) throws IOException {
+        postSummaryResultWithId(textContent);
+    }
+
+    /**
+     * Post a summary result comment and return the comment ID.
+     * @param textContent The markdown content to post
+     * @return The ID of the created comment
+     */
+    public String postSummaryResultWithId(String textContent) throws IOException {
         String workspace = vcsRepoInfo.getRepoWorkspace();
         String repoSlug = vcsRepoInfo.getRepoSlug();
 
@@ -65,6 +74,15 @@ public void postSummaryResult(String textContent) throws IOException {
 
         try (Response response = authorizedOkHttpClient.newCall(req).execute()) {
             validate(response);
+            // Parse response to get comment ID
+            if (response.body() != null) {
+                String responseBody = response.body().string();
+                JsonNode jsonNode = objectMapper.readTree(responseBody);
+                if (jsonNode.has("id")) {
+                    return String.valueOf(jsonNode.get("id").asInt());
+                }
+            }
+            return null;
         }
     }
 

java-ecosystem/libs/vcs-client/src/main/java/org/rostilos/codecrow/vcsclient/bitbucket/model/report/formatters/MarkdownAnalysisFormatter.java

@@ -30,12 +30,14 @@ public class MarkdownAnalysisFormatter implements AnalysisFormatter {
     );
 
     private final boolean useGitHubSpoilers;
+    private final boolean includeDetailedIssues;
 
     /**
-     * Default constructor - no spoilers (for Bitbucket)
+     * Default constructor - no spoilers (for Bitbucket), no detailed issues in summary
      */
     public MarkdownAnalysisFormatter() {
         this.useGitHubSpoilers = false;
+        this.includeDetailedIssues = false;
     }
 
     /**
@@ -44,6 +46,17 @@ public MarkdownAnalysisFormatter() {
      */
     public MarkdownAnalysisFormatter(boolean useGitHubSpoilers) {
         this.useGitHubSpoilers = useGitHubSpoilers;
+        this.includeDetailedIssues = false;
+    }
+
+    /**
+     * Full constructor with all options
+     * @param useGitHubSpoilers true for GitHub (uses details/summary), false for Bitbucket
+     * @param includeDetailedIssues true to include detailed issues in summary, false for separate comment
+     */
+    public MarkdownAnalysisFormatter(boolean useGitHubSpoilers, boolean includeDetailedIssues) {
+        this.useGitHubSpoilers = useGitHubSpoilers;
+        this.includeDetailedIssues = includeDetailedIssues;
     }
 
     @Override
@@ -104,15 +117,19 @@ public String format(AnalysisSummary summary) {
 
             md.append("\n");
 
-            md.append("### Detailed Issues\n\n");
+            // Only include detailed issues if explicitly requested
+            if (includeDetailedIssues) {
+                md.append("### Detailed Issues\n\n");
 
-            appendIssuesBySevertiy(md, summary.getIssues(), IssueSeverity.HIGH, EMOJI_HIGH, "High Severity Issues");
-            appendIssuesBySevertiy(md, summary.getIssues(), IssueSeverity.MEDIUM, EMOJI_MEDIUM, "Medium Severity Issues");
-            appendIssuesBySevertiy(md, summary.getIssues(), IssueSeverity.LOW, EMOJI_LOW, "Low Severity Issues");
-            appendIssuesBySevertiy(md, summary.getIssues(), IssueSeverity.INFO, EMOJI_INFO, "Informational Notes");
+                appendIssuesBySevertiy(md, summary.getIssues(), IssueSeverity.HIGH, EMOJI_HIGH, "High Severity Issues");
+                appendIssuesBySevertiy(md, summary.getIssues(), IssueSeverity.MEDIUM, EMOJI_MEDIUM, "Medium Severity Issues");
+                appendIssuesBySevertiy(md, summary.getIssues(), IssueSeverity.LOW, EMOJI_LOW, "Low Severity Issues");
+                appendIssuesBySevertiy(md, summary.getIssues(), IssueSeverity.INFO, EMOJI_INFO, "Informational Notes");
+            }
         }
 
-        if (!summary.getFileIssueCount().isEmpty()) {
+        // Only include files affected if detailed issues are included
+        if (includeDetailedIssues && !summary.getFileIssueCount().isEmpty()) {
             md.append("### Files Affected\n");
             summary.getFileIssueCount().entrySet().stream()
                     .sorted((a, b) -> b.getValue().compareTo(a.getValue()))
@@ -144,6 +161,58 @@ public String format(AnalysisSummary summary) {
         return md.toString();
     }
 
+    /**
+     * Format only the detailed issues section for posting as a separate comment.
+     * For GitHub, wraps all issues in a single collapsible spoiler.
+     * @param summary The analysis summary containing issues
+     * @return Markdown-formatted string with detailed issues, or empty string if no issues
+     */
+    public String formatDetailedIssues(AnalysisSummary summary) {
+        if (summary.getIssues() == null || summary.getIssues().isEmpty()) {
+            return "";
+        }
+
+        StringBuilder md = new StringBuilder();
+
+        int totalIssues = summary.getIssues().size();
+
+        if (useGitHubSpoilers) {
+            // GitHub: wrap ALL issues in a single collapsible section
+            md.append("<details>\n");
+            md.append(String.format("<summary><b>📋 Detailed Issues (%d)</b></summary>\n\n", totalIssues));
+        } else {
+            // Bitbucket: regular header (no spoiler support)
+            md.append("## 📋 Detailed Issues\n\n");
+        }
+
+        appendIssuesBySevertiy(md, summary.getIssues(), IssueSeverity.HIGH, EMOJI_HIGH, "High Severity Issues");
+        appendIssuesBySevertiy(md, summary.getIssues(), IssueSeverity.MEDIUM, EMOJI_MEDIUM, "Medium Severity Issues");
+        appendIssuesBySevertiy(md, summary.getIssues(), IssueSeverity.LOW, EMOJI_LOW, "Low Severity Issues");
+        appendIssuesBySevertiy(md, summary.getIssues(), IssueSeverity.INFO, EMOJI_INFO, "Informational Notes");
+
+        if (!summary.getFileIssueCount().isEmpty()) {
+            md.append("### Files Affected\n");
+            summary.getFileIssueCount().entrySet().stream()
+                    .sorted((a, b) -> b.getValue().compareTo(a.getValue()))
+                    .limit(10)
+                    .forEach(entry -> {
+                        String fileName = getShortFileName(entry.getKey());
+                        md.append(String.format("- **%s**: %d issue%s\n",
+                                fileName,
+                                entry.getValue(),
+                                entry.getValue() == 1 ? "" : "s"));
+                    });
+            md.append("\n");
+        }
+
+        if (useGitHubSpoilers) {
+            // Close the details tag for GitHub
+            md.append("</details>\n");
+        }
+
+        return md.toString();
+    }
+
     private void appendIssuesBySevertiy(StringBuilder md, List<AnalysisSummary.IssueSummary> issues,
                                         IssueSeverity severity, String emoji, String title) {
         List<AnalysisSummary.IssueSummary> severityIssues = issues.stream()

java-ecosystem/libs/vcs-client/src/main/java/org/rostilos/codecrow/vcsclient/bitbucket/service/ReportGenerator.java

@@ -213,6 +213,22 @@ public String createMarkdownSummary(CodeAnalysis analysis, AnalysisSummary summa
         }
     }
 
+    /**
+     * Creates markdown-formatted detailed issues for posting as a separate comment.
+     *
+     * @param summary The analysis summary
+     * @param useGitHubSpoilers true for GitHub (uses details/summary for collapsible fixes), false for Bitbucket
+     * @return Markdown-formatted string with detailed issues, or empty string if no issues
+     */
+    public String createDetailedIssuesMarkdown(AnalysisSummary summary, boolean useGitHubSpoilers) {
+        try {
+            return new MarkdownAnalysisFormatter(useGitHubSpoilers).formatDetailedIssues(summary);
+        } catch (Exception e) {
+            log.error("Error creating detailed issues markdown: {}", e.getMessage(), e);
+            return "";
+        }
+    }
+
     /**
      * Creates a plain text summary for pull request comments
      *

java-ecosystem/libs/vcs-client/src/main/java/org/rostilos/codecrow/vcsclient/github/actions/CommentOnPullRequestAction.java

@@ -200,4 +200,66 @@ public void deletePreviousComments(String owner, String repo, int prNumber, Stri
             }
         }
     }
+
+    /**
+     * Create a Pull Request Review with a summary body and optional inline comments.
+     * This creates a review that appears in the "Conversation" tab with connected comments.
+     * 
+     * @param owner Repository owner
+     * @param repo Repository name
+     * @param pullRequestNumber PR number
+     * @param commitId The SHA of the commit to review
+     * @param body The main review body/summary (appears as the review comment)
+     * @param event Review event: COMMENT, APPROVE, REQUEST_CHANGES
+     * @param comments List of inline comments, each with: path, line, body
+     * @return The review ID
+     */
+    public String createPullRequestReview(String owner, String repo, int pullRequestNumber,
+                                           String commitId, String body, String event,
+                                           List<Map<String, Object>> comments) throws IOException {
+        String apiUrl = String.format("%s/repos/%s/%s/pulls/%d/reviews",
+                GitHubConfig.API_BASE, owner, repo, pullRequestNumber);
+
+        Map<String, Object> payload = new HashMap<>();
+        payload.put("commit_id", commitId);
+        payload.put("body", body);
+        payload.put("event", event); // COMMENT, APPROVE, or REQUEST_CHANGES
+
+        if (comments != null && !comments.isEmpty()) {
+            payload.put("comments", comments);
+        }
+
+        Request req = new Request.Builder()
+                .url(apiUrl)
+                .header("Accept", "application/vnd.github+json")
+                .header("X-GitHub-Api-Version", "2022-11-28")
+                .post(RequestBody.create(objectMapper.writeValueAsString(payload), JSON))
+                .build();
+
+        log.debug("Creating PR review on GitHub: {}", apiUrl);
+
+        try (Response resp = authorizedOkHttpClient.newCall(req).execute()) {
+            if (!resp.isSuccessful()) {
+                String respBody = resp.body() != null ? resp.body().string() : "";
+                String msg = String.format("Failed to create PR review: %d - %s", resp.code(), respBody);
+                log.warn(msg);
+                throw new IOException(msg);
+            }
+
+            String respBody = resp.body() != null ? resp.body().string() : "";
+            Map<String, Object> responseMap = objectMapper.readValue(respBody, new TypeReference<Map<String, Object>>() {});
+            Number id = (Number) responseMap.get("id");
+            log.info("Created PR review {} on PR #{}", id, pullRequestNumber);
+            return id != null ? String.valueOf(id.longValue()) : null;
+        }
+    }
+
+    /**
+     * Create a simplified PR review with just summary and detailed issues body.
+     * Both will appear as connected review comments.
+     */
+    public String createReviewWithSummary(String owner, String repo, int pullRequestNumber,
+                                           String commitId, String summaryBody) throws IOException {
+        return createPullRequestReview(owner, repo, pullRequestNumber, commitId, summaryBody, "COMMENT", null);
+    }
 }

java-ecosystem/services/pipeline-agent/src/main/java/org/rostilos/codecrow/pipelineagent/service/bitbucket/BitbucketReportingService.java

@@ -33,6 +33,7 @@ public class BitbucketReportingService implements VcsReportingService {
     private static final Logger log = LoggerFactory.getLogger(BitbucketReportingService.class);
 
     private static final String CODECROW_REVIEW_MARKER = "<!-- codecrow-review -->";
+    private static final String CODECROW_ISSUES_MARKER = "<!-- codecrow-issues -->";
 
     private final ReportGenerator reportGenerator;
     private final VcsClientProvider vcsClientProvider;
@@ -121,6 +122,7 @@ public void postAnalysisResults(
 
         AnalysisSummary summary = reportGenerator.createAnalysisSummary(codeAnalysis, platformPrEntityId);
         String markdownSummary = reportGenerator.createMarkdownSummary(codeAnalysis, summary);
+        String detailedIssuesMarkdown = reportGenerator.createDetailedIssuesMarkdown(summary, false);
         CodeInsightsReport report = reportGenerator.createCodeInsightsReport(
                 summary,
                 codeAnalysis
@@ -136,14 +138,21 @@ public void postAnalysisResults(
                 vcsRepoInfo.getVcsConnection()
         );
 
-        postOrUpdateComment(httpClient, vcsRepoInfo, pullRequestNumber, markdownSummary, placeholderCommentId);
+        // Post summary comment (or update placeholder)
+        String summaryCommentId = postOrUpdateComment(httpClient, vcsRepoInfo, pullRequestNumber, markdownSummary, placeholderCommentId);
+
+        // Post detailed issues as a separate comment reply if there are issues
+        if (detailedIssuesMarkdown != null && !detailedIssuesMarkdown.isEmpty() && summaryCommentId != null) {
+            postDetailedIssuesReply(httpClient, vcsRepoInfo, pullRequestNumber, summaryCommentId, detailedIssuesMarkdown);
+        }
+
         postReport(httpClient, vcsRepoInfo, codeAnalysis.getCommitHash(), report);
         postAnnotations(httpClient, vcsRepoInfo, codeAnalysis.getCommitHash(), annotations);
 
         log.info("Successfully posted analysis results to Bitbucket");
     }
 
-    private void postOrUpdateComment(
+    private String postOrUpdateComment(
             OkHttpClient httpClient,
             VcsRepoInfo vcsRepoInfo,
             Long pullRequestNumber,
@@ -165,8 +174,34 @@ private void postOrUpdateComment(
             String fullContent = markdownSummary + "\n\n" + CODECROW_REVIEW_MARKER;
             commentAction.updateComment(placeholderCommentId, fullContent);
             log.debug("Updated placeholder comment {} with analysis results", placeholderCommentId);
+            return placeholderCommentId;
         } else {
-            commentAction.postSummaryResult(markdownSummary);
+            return commentAction.postSummaryResultWithId(markdownSummary);
+        }
+    }
+
+    private void postDetailedIssuesReply(
+            OkHttpClient httpClient,
+            VcsRepoInfo vcsRepoInfo,
+            Long pullRequestNumber,
+            String parentCommentId,
+            String detailedIssuesMarkdown
+    ) throws IOException {
+        try {
+            log.debug("Posting detailed issues as reply to comment {} on PR {}", parentCommentId, pullRequestNumber);
+
+            CommentOnBitbucketCloudAction commentAction = new CommentOnBitbucketCloudAction(
+                    httpClient,
+                    vcsRepoInfo,
+                    pullRequestNumber
+            );
+
+            String content = detailedIssuesMarkdown + "\n\n" + CODECROW_ISSUES_MARKER;
+            commentAction.postCommentReply(parentCommentId, content);
+
+            log.debug("Posted detailed issues reply to PR {}", pullRequestNumber);
+        } catch (Exception e) {
+            log.warn("Failed to post detailed issues as reply, will be included in annotations: {}", e.getMessage());
         }
     }