From 74af1dbc1ddcf39df15033abc354538adb3845a4 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 27 Feb 2026 04:49:23 +0000
Subject: [PATCH 01/16] Initial plan


From 07cb1a2af75b5b9bfa4fb99d21ca7224aee15ca5 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 27 Feb 2026 04:52:45 +0000
Subject: [PATCH 02/16] Add AI agent workflows for automatic issue and PR
 analysis

Co-authored-by: blackboxprogramming <118287761+blackboxprogramming@users.noreply.github.com>
---
 .github/workflows/issue-agent.yml |  82 ++++++++++++++++++++++
 .github/workflows/pr-agent.yml    | 109 ++++++++++++++++++++++++++++++
 2 files changed, 191 insertions(+)
 create mode 100644 .github/workflows/issue-agent.yml
 create mode 100644 .github/workflows/pr-agent.yml

diff --git a/.github/workflows/issue-agent.yml b/.github/workflows/issue-agent.yml
new file mode 100644
index 0000000..d7a45ee
--- /dev/null
+++ b/.github/workflows/issue-agent.yml
@@ -0,0 +1,82 @@
+name: Issue Agent
+
+on:
+  issues:
+    types: [opened, edited, reopened, labeled]
+
+permissions:
+  issues: write
+  models: read
+
+jobs:
+  analyze-issue:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Analyze issue and post comment
+        uses: actions/github-script@v7
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          script: |
+            const issueNumber = context.issue.number;
+            const issueTitle = context.payload.issue.title;
+            const issueBody  = context.payload.issue.body || '(no description provided)';
+            const issueUser  = context.payload.issue.user.login;
+            const labels     = (context.payload.issue.labels || []).map(l => l.name).join(', ') || 'none';
+
+            // Call GitHub Models API for AI-powered analysis
+            const response = await fetch('https://models.inference.ai.azure.com/chat/completions', {
+              method: 'POST',
+              headers: {
+                'Content-Type': 'application/json',
+                'Authorization': `Bearer ${process.env.GITHUB_TOKEN}`
+              },
+              body: JSON.stringify({
+                model: 'gpt-4o-mini',
+                messages: [
+                  {
+                    role: 'system',
+                    content: `You are a rigorous technical agent reviewing GitHub issues for the "simulation-theory" repository — a research project on simulation theory, mathematics, quantum mechanics, and philosophy. Your job is to carefully read each issue and provide a thorough, structured analysis.
+
+For each issue produce:
+1. **Summary** — a concise one-paragraph summary of what the issue is about.
+2. **Key Points** — bullet list of the most important observations or questions raised.
+3. **Relevance to Simulation Theory** — how this issue connects to the project's themes.
+4. **Suggested Actions** — concrete next steps or questions for the author.
+
+Be rigorous, thoughtful, and constructive. Keep the tone academic and helpful.`
+                  },
+                  {
+                    role: 'user',
+                    content: `Please analyze this GitHub issue:\n\n**Title:** ${issueTitle}\n**Author:** ${issueUser}\n**Labels:** ${labels}\n\n**Description:**\n${issueBody}`
+                  }
+                ],
+                max_tokens: 1500,
+                temperature: 0.4
+              })
+            });
+
+            let analysisText;
+            if (response.ok) {
+              const data = await response.json();
+              if (data.choices && data.choices.length > 0 && data.choices[0].message) {
+                analysisText = data.choices[0].message.content;
+              } else {
+                console.log('Unexpected response structure from GitHub Models API:', JSON.stringify(data));
+              }
+            } else {
+              console.log(`GitHub Models API returned ${response.status}: ${await response.text()}`);
+            }
+
+            // Fallback: structured analysis without AI
+            if (!analysisText) {
+              analysisText = `**Summary**\nIssue #${issueNumber} titled *"${issueTitle}"* was submitted by @${issueUser}. ${issueBody.length > 0 ? 'It contains a description that may include images or text.' : 'No description was provided.'}\n\n**Labels:** ${labels}\n\n**Suggested Actions**\n- Review the content of this issue and add appropriate labels if missing.\n- Respond to the author with any clarifying questions.\n- Link related issues or pull requests if applicable.`;
+            }
+
+            const comment = `## 🤖 Agent Analysis\n\n${analysisText}\n\n---\n*This comment was generated automatically by the Issue Agent workflow.*`;
+
+            await github.rest.issues.createComment({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number: issueNumber,
+              body: comment
+            });
diff --git a/.github/workflows/pr-agent.yml b/.github/workflows/pr-agent.yml
new file mode 100644
index 0000000..74ca45b
--- /dev/null
+++ b/.github/workflows/pr-agent.yml
@@ -0,0 +1,109 @@
+name: PR Agent
+
+on:
+  pull_request:
+    types: [opened, edited, synchronize, reopened]
+
+permissions:
+  pull-requests: write
+  contents: read
+  models: read
+
+jobs:
+  analyze-pr:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Collect changed files
+        id: changed
+        run: |
+          BASE="${{ github.event.pull_request.base.sha }}"
+          HEAD="${{ github.event.pull_request.head.sha }}"
+          ALL_FILES=$(git diff --name-only "$BASE" "$HEAD" 2>/dev/null)
+          TOTAL=$(echo "$ALL_FILES" | grep -c . || echo 0)
+          FILES=$(echo "$ALL_FILES" | head -50 | tr '\n' ', ')
+          if [ "$TOTAL" -gt 50 ]; then
+            REMAINING=$(( TOTAL - 50 ))
+            FILES="${FILES} (and ${REMAINING} more files)"
+          fi
+          echo "files=$FILES" >> "$GITHUB_OUTPUT"
+
+      - name: Analyze PR and post comment
+        uses: actions/github-script@v7
+        env:
+          CHANGED_FILES: ${{ steps.changed.outputs.files }}
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          script: |
+            const prNumber    = context.payload.pull_request.number;
+            const prTitle     = context.payload.pull_request.title;
+            const prBody      = context.payload.pull_request.body || '(no description provided)';
+            const prUser      = context.payload.pull_request.user.login;
+            const baseBranch  = context.payload.pull_request.base.ref;
+            const headBranch  = context.payload.pull_request.head.ref;
+            const changedFiles = process.env.CHANGED_FILES || 'unknown';
+            const additions   = context.payload.pull_request.additions ?? '?';
+            const deletions   = context.payload.pull_request.deletions ?? '?';
+
+            // Call GitHub Models API for AI-powered analysis
+            const response = await fetch('https://models.inference.ai.azure.com/chat/completions', {
+              method: 'POST',
+              headers: {
+                'Content-Type': 'application/json',
+                'Authorization': `Bearer ${process.env.GITHUB_TOKEN}`
+              },
+              body: JSON.stringify({
+                model: 'gpt-4o-mini',
+                messages: [
+                  {
+                    role: 'system',
+                    content: `You are a rigorous code and content review agent for the "simulation-theory" repository — a research project on simulation theory, mathematics, quantum mechanics, and philosophy. Your job is to carefully examine each pull request and provide a thorough, structured review.
+
+For each PR produce:
+1. **Summary** — a concise one-paragraph summary of the proposed changes.
+2. **Changed Files Analysis** — observations about the files being modified and why they matter.
+3. **Potential Concerns** — any risks, conflicts, or issues the reviewer should check.
+4. **Relevance to Project Goals** — how these changes align with (or diverge from) simulation-theory research.
+5. **Suggested Actions** — specific things the PR author or reviewers should do before merging.
+
+Be rigorous, constructive, and precise. Keep the tone academic and professional.`
+                  },
+                  {
+                    role: 'user',
+                    content: `Please analyze this pull request:\n\n**Title:** ${prTitle}\n**Author:** ${prUser}\n**Base branch:** ${baseBranch} ← **Head branch:** ${headBranch}\n**Changes:** +${additions} / -${deletions} lines\n**Changed files:** ${changedFiles}\n\n**Description:**\n${prBody}`
+                  }
+                ],
+                max_tokens: 1500,
+                temperature: 0.4
+              })
+            });
+
+            let analysisText;
+            if (response.ok) {
+              const data = await response.json();
+              if (data.choices && data.choices.length > 0 && data.choices[0].message) {
+                analysisText = data.choices[0].message.content;
+              } else {
+                console.log('Unexpected response structure from GitHub Models API:', JSON.stringify(data));
+              }
+            } else {
+              console.log(`GitHub Models API returned ${response.status}: ${await response.text()}`);
+            }
+
+            // Fallback: structured analysis without AI
+            if (!analysisText) {
+              analysisText = `**Summary**\nPR #${prNumber} titled *"${prTitle}"* was submitted by @${prUser} merging \`${headBranch}\` into \`${baseBranch}\`.\n\n**Changed Files**\n${changedFiles || 'No files listed.'}\n\n**Stats:** +${additions} additions / -${deletions} deletions\n\n**Suggested Actions**\n- Review all changed files for correctness and consistency.\n- Ensure the description clearly explains the motivation for each change.\n- Verify no unintended files are included in this PR.`;
+            }
+
+            const comment = `## 🤖 Agent Review\n\n${analysisText}\n\n---\n*This comment was generated automatically by the PR Agent workflow.*`;
+
+            await github.rest.issues.createComment({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number: prNumber,
+              body: comment
+            });

From 4f4c9e919dcd78758280218ae1858c5fea844096 Mon Sep 17 00:00:00 2001
From: Alexa Amundson <118287761+blackboxprogramming@users.noreply.github.com>
Date: Fri, 27 Feb 2026 01:43:41 -0600
Subject: [PATCH 03/16] Update issue-agent.yml

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 .github/workflows/issue-agent.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/issue-agent.yml b/.github/workflows/issue-agent.yml
index d7a45ee..eceef72 100644
--- a/.github/workflows/issue-agent.yml
+++ b/.github/workflows/issue-agent.yml
@@ -6,7 +6,6 @@ on:
 
 permissions:
   issues: write
-  models: read
 
 jobs:
   analyze-issue:

From bb7f155dade231b5e3016e0349a82d0a838f00c7 Mon Sep 17 00:00:00 2001
From: Alexa Amundson <118287761+blackboxprogramming@users.noreply.github.com>
Date: Fri, 27 Feb 2026 01:44:00 -0600
Subject: [PATCH 04/16] Update issue-agent.yml

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 .github/workflows/issue-agent.yml | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/issue-agent.yml b/.github/workflows/issue-agent.yml
index eceef72..eec1f4f 100644
--- a/.github/workflows/issue-agent.yml
+++ b/.github/workflows/issue-agent.yml
@@ -56,10 +56,16 @@ Be rigorous, thoughtful, and constructive. Keep the tone academic and helpful.`
 
             let analysisText;
             if (response.ok) {
-              const data = await response.json();
-              if (data.choices && data.choices.length > 0 && data.choices[0].message) {
+              let data;
+              try {
+                data = await response.json();
+              } catch (error) {
+                console.log('Failed to parse JSON from GitHub Models API response:', error);
+              }
+
+              if (data && data.choices && data.choices.length > 0 && data.choices[0].message) {
                 analysisText = data.choices[0].message.content;
-              } else {
+              } else if (data) {
                 console.log('Unexpected response structure from GitHub Models API:', JSON.stringify(data));
               }
             } else {

From 6d6bc2e962dcf053fecff8099d6cd173cf32b304 Mon Sep 17 00:00:00 2001
From: Alexa Amundson <118287761+blackboxprogramming@users.noreply.github.com>
Date: Fri, 27 Feb 2026 01:44:15 -0600
Subject: [PATCH 05/16] Update issue-agent.yml

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 .github/workflows/issue-agent.yml | 31 ++++++++++++++++++++++++++++---
 1 file changed, 28 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/issue-agent.yml b/.github/workflows/issue-agent.yml
index eec1f4f..803d657 100644
--- a/.github/workflows/issue-agent.yml
+++ b/.github/workflows/issue-agent.yml
@@ -77,11 +77,36 @@ Be rigorous, thoughtful, and constructive. Keep the tone academic and helpful.`
               analysisText = `**Summary**\nIssue #${issueNumber} titled *"${issueTitle}"* was submitted by @${issueUser}. ${issueBody.length > 0 ? 'It contains a description that may include images or text.' : 'No description was provided.'}\n\n**Labels:** ${labels}\n\n**Suggested Actions**\n- Review the content of this issue and add appropriate labels if missing.\n- Respond to the author with any clarifying questions.\n- Link related issues or pull requests if applicable.`;
             }
 
-            const comment = `## 🤖 Agent Analysis\n\n${analysisText}\n\n---\n*This comment was generated automatically by the Issue Agent workflow.*`;
+            const marker = '*This comment was generated automatically by the Issue Agent workflow.*';
+            const commentBody = `## 🤖 Agent Analysis\n\n${analysisText}\n\n---\n${marker}`;
 
-            await github.rest.issues.createComment({
+            // Look for an existing Issue Agent comment and update it if found to avoid spamming
+            const { data: existingComments } = await github.rest.issues.listComments({
               owner: context.repo.owner,
               repo: context.repo.repo,
               issue_number: issueNumber,
-              body: comment
+              per_page: 100
             });
+
+            const existingAgentComment = existingComments.find(c =>
+              c.user &&
+              c.user.type === 'Bot' &&
+              typeof c.body === 'string' &&
+              c.body.includes(marker)
+            );
+
+            if (existingAgentComment) {
+              await github.rest.issues.updateComment({
+                owner: context.repo.owner,
+                repo: context.repo.repo,
+                comment_id: existingAgentComment.id,
+                body: commentBody
+              });
+            } else {
+              await github.rest.issues.createComment({
+                owner: context.repo.owner,
+                repo: context.repo.repo,
+                issue_number: issueNumber,
+                body: commentBody
+              });
+            }

From e76d0c8ec40076dd87c307c7c487e4f0c468f09f Mon Sep 17 00:00:00 2001
From: Alexa Amundson <118287761+blackboxprogramming@users.noreply.github.com>
Date: Fri, 27 Feb 2026 01:44:23 -0600
Subject: [PATCH 06/16] Update pr-agent.yml

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 .github/workflows/pr-agent.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pr-agent.yml b/.github/workflows/pr-agent.yml
index 74ca45b..98a7aa0 100644
--- a/.github/workflows/pr-agent.yml
+++ b/.github/workflows/pr-agent.yml
@@ -1,7 +1,7 @@
 name: PR Agent
 
 on:
-  pull_request:
+  pull_request_target:
     types: [opened, edited, synchronize, reopened]
 
 permissions:

From da577bc0152e45b009c6379e45cfe6f7db88c3d9 Mon Sep 17 00:00:00 2001
From: Alexa Amundson <118287761+blackboxprogramming@users.noreply.github.com>
Date: Fri, 27 Feb 2026 01:44:29 -0600
Subject: [PATCH 07/16] Update pr-agent.yml

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 .github/workflows/pr-agent.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pr-agent.yml b/.github/workflows/pr-agent.yml
index 98a7aa0..9f1e55a 100644
--- a/.github/workflows/pr-agent.yml
+++ b/.github/workflows/pr-agent.yml
@@ -2,7 +2,7 @@ name: PR Agent
 
 on:
   pull_request_target:
-    types: [opened, edited, synchronize, reopened]
+    types: [opened, reopened]
 
 permissions:
   pull-requests: write

From 601d02414c7592834f206378cd7c0a37058f3b73 Mon Sep 17 00:00:00 2001
From: Alexa Amundson <118287761+blackboxprogramming@users.noreply.github.com>
Date: Fri, 27 Feb 2026 01:44:44 -0600
Subject: [PATCH 08/16] Update pr-agent.yml

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 .github/workflows/pr-agent.yml | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pr-agent.yml b/.github/workflows/pr-agent.yml
index 9f1e55a..48bddb9 100644
--- a/.github/workflows/pr-agent.yml
+++ b/.github/workflows/pr-agent.yml
@@ -21,10 +21,20 @@ jobs:
       - name: Collect changed files
         id: changed
         run: |
+          # Ensure the base branch ref is available locally (important for fork-based PRs)
+          git fetch origin "${{ github.event.pull_request.base.ref }}" --no-tags --prune --depth=1
+
           BASE="${{ github.event.pull_request.base.sha }}"
           HEAD="${{ github.event.pull_request.head.sha }}"
-          ALL_FILES=$(git diff --name-only "$BASE" "$HEAD" 2>/dev/null)
-          TOTAL=$(echo "$ALL_FILES" | grep -c . || echo 0)
+
+          # Compute the list of changed files between base and head; fail explicitly on error
+          if ! ALL_FILES=$(git diff --name-only "$BASE" "$HEAD"); then
+            echo "Error: failed to compute git diff between $BASE and $HEAD" >&2
+            exit 1
+          fi
+
+          # Count total changed files robustly, even when there are zero files
+          TOTAL=$(printf '%s\n' "$ALL_FILES" | sed '/^$/d' | wc -l | tr -d ' ')
           FILES=$(echo "$ALL_FILES" | head -50 | tr '\n' ', ')
           if [ "$TOTAL" -gt 50 ]; then
             REMAINING=$(( TOTAL - 50 ))

From 80c513a5bff60ed2e296a0bd63b8728361d967ad Mon Sep 17 00:00:00 2001
From: Alexa Amundson <118287761+blackboxprogramming@users.noreply.github.com>
Date: Fri, 27 Feb 2026 01:44:51 -0600
Subject: [PATCH 09/16] Update pr-agent.yml

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 .github/workflows/pr-agent.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/pr-agent.yml b/.github/workflows/pr-agent.yml
index 48bddb9..0c5825a 100644
--- a/.github/workflows/pr-agent.yml
+++ b/.github/workflows/pr-agent.yml
@@ -36,6 +36,7 @@ jobs:
           # Count total changed files robustly, even when there are zero files
           TOTAL=$(printf '%s\n' "$ALL_FILES" | sed '/^$/d' | wc -l | tr -d ' ')
           FILES=$(echo "$ALL_FILES" | head -50 | tr '\n' ', ')
+          FILES="${FILES%, }"
           if [ "$TOTAL" -gt 50 ]; then
             REMAINING=$(( TOTAL - 50 ))
             FILES="${FILES} (and ${REMAINING} more files)"

From d826b372e5a730565e8752fa8144bfdef90431bc Mon Sep 17 00:00:00 2001
From: Alexa Amundson <118287761+blackboxprogramming@users.noreply.github.com>
Date: Fri, 27 Feb 2026 01:45:01 -0600
Subject: [PATCH 10/16] Update pr-agent.yml

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 .github/workflows/pr-agent.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pr-agent.yml b/.github/workflows/pr-agent.yml
index 0c5825a..e5f328b 100644
--- a/.github/workflows/pr-agent.yml
+++ b/.github/workflows/pr-agent.yml
@@ -41,7 +41,11 @@ jobs:
             REMAINING=$(( TOTAL - 50 ))
             FILES="${FILES} (and ${REMAINING} more files)"
           fi
-          echo "files=$FILES" >> "$GITHUB_OUTPUT"
+          {
+            echo 'files<<EOF'
+            echo "$FILES"
+            echo 'EOF'
+          } >> "$GITHUB_OUTPUT"
 
       - name: Analyze PR and post comment
         uses: actions/github-script@v7

From 4c01769a17277b97f95acb6a65f56f848624908c Mon Sep 17 00:00:00 2001
From: Alexa Amundson <118287761+blackboxprogramming@users.noreply.github.com>
Date: Fri, 27 Feb 2026 01:45:25 -0600
Subject: [PATCH 11/16] Update pr-agent.yml

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 .github/workflows/pr-agent.yml | 26 ++++++++++++++------------
 1 file changed, 14 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/pr-agent.yml b/.github/workflows/pr-agent.yml
index e5f328b..cb8757f 100644
--- a/.github/workflows/pr-agent.yml
+++ b/.github/workflows/pr-agent.yml
@@ -65,18 +65,20 @@ jobs:
             const deletions   = context.payload.pull_request.deletions ?? '?';
 
             // Call GitHub Models API for AI-powered analysis
-            const response = await fetch('https://models.inference.ai.azure.com/chat/completions', {
-              method: 'POST',
-              headers: {
-                'Content-Type': 'application/json',
-                'Authorization': `Bearer ${process.env.GITHUB_TOKEN}`
-              },
-              body: JSON.stringify({
-                model: 'gpt-4o-mini',
-                messages: [
-                  {
-                    role: 'system',
-                    content: `You are a rigorous code and content review agent for the "simulation-theory" repository — a research project on simulation theory, mathematics, quantum mechanics, and philosophy. Your job is to carefully examine each pull request and provide a thorough, structured review.
+            let response;
+            try {
+              response = await fetch('https://models.inference.ai.azure.com/chat/completions', {
+                method: 'POST',
+                headers: {
+                  'Content-Type': 'application/json',
+                  'Authorization': `Bearer ${process.env.GITHUB_TOKEN}`
+                },
+                body: JSON.stringify({
+                  model: 'gpt-4o-mini',
+                  messages: [
+                    {
+                      role: 'system',
+                      content: `You are a rigorous code and content review agent for the "simulation-theory" repository — a research project on simulation theory, mathematics, quantum mechanics, and philosophy. Your job is to carefully examine each pull request and provide a thorough, structured review.
 
 For each PR produce:
 1. **Summary** — a concise one-paragraph summary of the proposed changes.

From 42eb3caf4602cde435ab5e9703dbfd77174450fe Mon Sep 17 00:00:00 2001
From: Alexa Amundson <118287761+blackboxprogramming@users.noreply.github.com>
Date: Fri, 27 Feb 2026 01:45:45 -0600
Subject: [PATCH 12/16] Update pr-agent.yml

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 .github/workflows/pr-agent.yml | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/pr-agent.yml b/.github/workflows/pr-agent.yml
index cb8757f..82016de 100644
--- a/.github/workflows/pr-agent.yml
+++ b/.github/workflows/pr-agent.yml
@@ -101,11 +101,15 @@ Be rigorous, constructive, and precise. Keep the tone academic and professional.
 
             let analysisText;
             if (response.ok) {
-              const data = await response.json();
-              if (data.choices && data.choices.length > 0 && data.choices[0].message) {
-                analysisText = data.choices[0].message.content;
-              } else {
-                console.log('Unexpected response structure from GitHub Models API:', JSON.stringify(data));
+              try {
+                const data = await response.json();
+                if (data.choices && data.choices.length > 0 && data.choices[0].message) {
+                  analysisText = data.choices[0].message.content;
+                } else {
+                  console.log('Unexpected response structure from GitHub Models API:', JSON.stringify(data));
+                }
+              } catch (error) {
+                console.log('Failed to parse JSON response from GitHub Models API:', error);
               }
             } else {
               console.log(`GitHub Models API returned ${response.status}: ${await response.text()}`);

From 08d29744cff8d1bef96d1ff2d5d60dcb2ec9c011 Mon Sep 17 00:00:00 2001
From: Alexa Amundson <118287761+blackboxprogramming@users.noreply.github.com>
Date: Fri, 27 Feb 2026 01:45:54 -0600
Subject: [PATCH 13/16] Update pr-agent.yml

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 .github/workflows/pr-agent.yml | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/pr-agent.yml b/.github/workflows/pr-agent.yml
index 82016de..0b36873 100644
--- a/.github/workflows/pr-agent.yml
+++ b/.github/workflows/pr-agent.yml
@@ -104,15 +104,19 @@ Be rigorous, constructive, and precise. Keep the tone academic and professional.
               try {
                 const data = await response.json();
                 if (data.choices && data.choices.length > 0 && data.choices[0].message) {
+            try {
+              if (response.ok) {
+                const data = await response.json();
+                if (data.choices && data.choices.length > 0 && data.choices[0].message) {
                   analysisText = data.choices[0].message.content;
                 } else {
                   console.log('Unexpected response structure from GitHub Models API:', JSON.stringify(data));
                 }
-              } catch (error) {
-                console.log('Failed to parse JSON response from GitHub Models API:', error);
+              } else {
+                console.log(`GitHub Models API returned ${response.status}: ${await response.text()}`);
               }
-            } else {
-              console.log(`GitHub Models API returned ${response.status}: ${await response.text()}`);
+            } catch (error) {
+              console.log('Error while calling or parsing response from GitHub Models API, falling back to templated analysis:', error);
             }
 
             // Fallback: structured analysis without AI

From 7b8fb9a4518ddd6b52e8ef28da34a7f4daf46269 Mon Sep 17 00:00:00 2001
From: Alexa Amundson <118287761+blackboxprogramming@users.noreply.github.com>
Date: Fri, 27 Feb 2026 01:46:07 -0600
Subject: [PATCH 14/16] Update pr-agent.yml

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 .github/workflows/pr-agent.yml | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pr-agent.yml b/.github/workflows/pr-agent.yml
index 0b36873..67239a5 100644
--- a/.github/workflows/pr-agent.yml
+++ b/.github/workflows/pr-agent.yml
@@ -121,7 +121,18 @@ Be rigorous, constructive, and precise. Keep the tone academic and professional.
 
             // Fallback: structured analysis without AI
             if (!analysisText) {
-              analysisText = `**Summary**\nPR #${prNumber} titled *"${prTitle}"* was submitted by @${prUser} merging \`${headBranch}\` into \`${baseBranch}\`.\n\n**Changed Files**\n${changedFiles || 'No files listed.'}\n\n**Stats:** +${additions} additions / -${deletions} deletions\n\n**Suggested Actions**\n- Review all changed files for correctness and consistency.\n- Ensure the description clearly explains the motivation for each change.\n- Verify no unintended files are included in this PR.`;
+              let changedFilesSection;
+              if (!changedFiles || changedFiles === 'unknown') {
+                changedFilesSection = 'No changed file list is available for this PR.';
+              } else {
+                const files = changedFiles.split(',').map(f => f.trim()).filter(f => f.length > 0);
+                if (files.length === 0) {
+                  changedFilesSection = 'No files listed.';
+                } else {
+                  changedFilesSection = files.map(f => `- ${f}`).join('\n');
+                }
+              }
+              analysisText = `**Summary**\nPR #${prNumber} titled *"${prTitle}"* was submitted by @${prUser} merging \`${headBranch}\` into \`${baseBranch}\`.\n\n**Changed Files**\n${changedFilesSection}\n\n**Stats:** +${additions} additions / -${deletions} deletions\n\n**Suggested Actions**\n- Review all changed files for correctness and consistency.\n- Ensure the description clearly explains the motivation for each change.\n- Verify no unintended files are included in this PR.`;
             }
 
             const comment = `## 🤖 Agent Review\n\n${analysisText}\n\n---\n*This comment was generated automatically by the PR Agent workflow.*`;

From ada719d09a5b9e5fa409aa793645c11d08fd37a3 Mon Sep 17 00:00:00 2001
From: Alexa Amundson <118287761+blackboxprogramming@users.noreply.github.com>
Date: Fri, 27 Feb 2026 01:46:26 -0600
Subject: [PATCH 15/16] Update pr-agent.yml

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 .github/workflows/pr-agent.yml | 21 ++++++++++++++++++++-
 1 file changed, 20 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pr-agent.yml b/.github/workflows/pr-agent.yml
index 67239a5..ea1df68 100644
--- a/.github/workflows/pr-agent.yml
+++ b/.github/workflows/pr-agent.yml
@@ -135,8 +135,27 @@ Be rigorous, constructive, and precise. Keep the tone academic and professional.
               analysisText = `**Summary**\nPR #${prNumber} titled *"${prTitle}"* was submitted by @${prUser} merging \`${headBranch}\` into \`${baseBranch}\`.\n\n**Changed Files**\n${changedFilesSection}\n\n**Stats:** +${additions} additions / -${deletions} deletions\n\n**Suggested Actions**\n- Review all changed files for correctness and consistency.\n- Ensure the description clearly explains the motivation for each change.\n- Verify no unintended files are included in this PR.`;
             }
 
-            const comment = `## 🤖 Agent Review\n\n${analysisText}\n\n---\n*This comment was generated automatically by the PR Agent workflow.*`;
+            // Sanitize and limit the AI-generated analysis text before posting as a comment.
+            const MAX_COMMENT_LENGTH = 5000;
+            const sanitizeAnalysisText = (text) => {
+              if (typeof text !== 'string') {
+                return '';
+              }
+              // Remove script-like tags and generic HTML tags as a defense-in-depth measure.
+              let cleaned = text
+                .replace(/<\s*\/?\s*script[^>]*>/gi, '')
+                .replace(/<[^>]+>/g, '')
+                .trim();
+              if (cleaned.length > MAX_COMMENT_LENGTH) {
+                cleaned = cleaned.slice(0, MAX_COMMENT_LENGTH) +
+                  '\n\n*Note: Output truncated to fit comment length limits.*';
+              }
+              return cleaned;
+            };
+
+            const safeAnalysisText = sanitizeAnalysisText(analysisText);
 
+            const comment = `## 🤖 Agent Review\n\n${safeAnalysisText}\n\n---\n*This comment was generated automatically by the PR Agent workflow.*`;
             await github.rest.issues.createComment({
               owner: context.repo.owner,
               repo: context.repo.repo,

From 4a41d443d8e6634cc7e3fa63d774bf41eadf6ad4 Mon Sep 17 00:00:00 2001
From: Alexa Amundson <118287761+blackboxprogramming@users.noreply.github.com>
Date: Fri, 27 Feb 2026 01:46:41 -0600
Subject: [PATCH 16/16] Update pr-agent.yml

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 .github/workflows/pr-agent.yml | 28 +++++++++++++++++++++++++---
 1 file changed, 25 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pr-agent.yml b/.github/workflows/pr-agent.yml
index ea1df68..42dc929 100644
--- a/.github/workflows/pr-agent.yml
+++ b/.github/workflows/pr-agent.yml
@@ -156,9 +156,31 @@ Be rigorous, constructive, and precise. Keep the tone academic and professional.
             const safeAnalysisText = sanitizeAnalysisText(analysisText);
 
             const comment = `## 🤖 Agent Review\n\n${safeAnalysisText}\n\n---\n*This comment was generated automatically by the PR Agent workflow.*`;
-            await github.rest.issues.createComment({
+            // Try to find an existing PR Agent comment to update, to avoid spamming the thread
+            const { data: existingComments } = await github.rest.issues.listComments({
               owner: context.repo.owner,
               repo: context.repo.repo,
-              issue_number: prNumber,
-              body: comment
+              issue_number: prNumber
             });
+
+            const existingAgentComment = existingComments.find(c =>
+              c &&
+              c.body &&
+              c.body.includes('This comment was generated automatically by the PR Agent workflow.')
+            );
+
+            if (existingAgentComment) {
+              await github.rest.issues.updateComment({
+                owner: context.repo.owner,
+                repo: context.repo.repo,
+                comment_id: existingAgentComment.id,
+                body: comment
+              });
+            } else {
+              await github.rest.issues.createComment({
+                owner: context.repo.owner,
+                repo: context.repo.repo,
+                issue_number: prNumber,
+                body: comment
+              });
+            }