fix: robust end-to-end evolution pipeline — 10 bug fixes

- evolve.sh: replace dangerous git commit --amend with safe separate commit for DAY_COUNT
- evolve.sh: fallback merge now detects conflicts and aborts instead of swallowing with || true
- phases_communicate.go: journal timeout uses parent ctx instead of context.Background()
- git.go: remove --admin flag that bypassed branch protection on conflict
- git.go: quote branch name in push command to prevent shell injection
- engine.go: log error from handleCommitAndPR instead of silently swallowing it
- engine.go: fix wrong buildUserMessage() passed as learning context (use empty string)
- phases.go: log verifyProtected errors instead of discarding with _
- phases.go: add conventional commit format guidance to agent prompt (fixes "test message")
- analysis.go: fix string(rune('0'+count)) → strconv.Itoa(count) (broken for counts > 9)

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: Patel230

internal/evolution/analysis.go

@@ -4,6 +4,7 @@ import (
 	"os/exec"
 	"path/filepath"
 	"sort"
+	"strconv"
 	"strings"
 )
 
@@ -144,7 +145,7 @@ func findHotspots(repoPath string) []string {
 		limit = len(entries)
 	}
 	for _, e := range entries[:limit] {
-		results = append(results, e.name+" (changed "+string(rune('0'+e.count))+"x)")
+		results = append(results, e.name+" (changed "+strconv.Itoa(e.count)+"x)")
 	}
 	return results
 }

internal/evolution/engine.go

@@ -192,6 +192,7 @@ func (e *Engine) handlePostRunTests(ctx context.Context, day int, output string,
 
 	e.logger.Info("tests passed, creating feature branch")
 	if err := e.handleCommitAndPR(ctx, day, output, p, result); err != nil {
+		e.logger.Warn("commit/PR flow failed, continuing", "err", err)
 		return nil
 	}
 
@@ -365,7 +366,7 @@ func (e *Engine) handlePRReviewAndMerge(ctx context.Context, p iteragent.Provide
 	result.Status = "merged"
 	result.PRNumber = e.prNumber
 	result.PRURL = e.prURL
-	_ = e.appendLearningJSONL(firstLine(extractCommitMessage(output)), "evolution", buildUserMessage(e.repoPath, "", ""), "")
+	_ = e.appendLearningJSONL(firstLine(extractCommitMessage(output)), "evolution", "", "")
 	e.appendJournal(result, output, p.Name(), true)
 
 	_ = e.switchToMain(ctx)

internal/evolution/git.go

@@ -94,7 +94,7 @@ func (e *Engine) createFeatureBranch(ctx context.Context, day int) (string, erro
 
 func (e *Engine) pushBranch(ctx context.Context) error {
 	_, err := e.runTool(ctx, "bash", map[string]string{
-		"cmd": fmt.Sprintf("git push -u origin %s", e.branchName),
+		"cmd": fmt.Sprintf("git push -u origin %q", e.branchName),
 	})
 	return err
 }
@@ -205,16 +205,6 @@ func (e *Engine) mergePR(ctx context.Context) error {
 		"cmd": fmt.Sprintf("gh pr merge %d --repo %s --squash --delete-branch", e.prNumber, e.repo),
 	})
 	if err != nil {
-		if strings.Contains(strings.ToLower(out), "no mergeable") || strings.Contains(strings.ToLower(out), "conflict") {
-			e.logger.Warn("PR has merge conflicts, attempting merge with --admin flag (bypasses branch protection)", "pr", e.prNumber)
-			mergeOut, mergeErr := e.runTool(ctx, "bash", map[string]string{
-				"cmd": fmt.Sprintf("gh pr merge %d --repo %s --squash --admin --delete-branch 2>&1 || echo 'MERGE_FAILED'", e.prNumber, e.repo),
-			})
-			if mergeErr != nil || strings.Contains(mergeOut, "MERGE_FAILED") {
-				e.logger.Warn("PR merge failed, will retry next session", "output", mergeOut)
-				return fmt.Errorf("merge conflict: %s", mergeOut)
-			}
-		}
 		return fmt.Errorf("PR merge failed: %w, output: %s", err, out)
 	}
 

internal/evolution/phases.go

@@ -198,7 +198,7 @@ func (e *Engine) runTaskAttempt(ctx context.Context, p iteragent.Provider, task
 	if extraContext != "" {
 		userMsg += "\n\n" + extraContext
 	}
-	userMsg += "\n\nAfter implementing, run: go build ./... && go test ./...\nThen commit your changes."
+	userMsg += "\n\nAfter implementing, run: go build ./... && go test ./...\nThen commit your changes using a conventional commit message (e.g. feat: ..., fix: ..., chore: ..., refactor: ..., test: ..., docs: ...)."
 
 	a := e.newAgent(p, tools, systemPrompt, skills)
 	var taskOutput string
@@ -219,7 +219,9 @@ func (e *Engine) runTaskAttempt(ctx context.Context, p iteragent.Provider, task
 		return false, fmt.Sprintf("Agent error: %s", taskErr)
 	}
 
-	if violations, _ := e.verifyProtected(ctx); len(violations) > 0 {
+	if violations, err := e.verifyProtected(ctx); err != nil {
+		e.logger.Warn("verifyProtected check failed", "err", err)
+	} else if len(violations) > 0 {
 		e.logger.Warn("protected files modified, reverting", "number", task.Number, "files", violations)
 		_ = e.revert(ctx)
 		return false, fmt.Sprintf("Protected files were modified (not allowed): %v", violations)

internal/evolution/phases_communicate.go

@@ -61,7 +61,7 @@ func (e *Engine) readDayCount() string {
 
 // writeJournalEntry always produces a journal entry — via agent or fallback.
 func (e *Engine) writeJournalEntry(ctx context.Context, p iteragent.Provider, day string) {
-	journalCtx, cancel := context.WithTimeout(context.Background(), 2*time.Minute)
+	journalCtx, cancel := context.WithTimeout(ctx, 2*time.Minute)
 	defer cancel()
 
 	recentCommits, _ := e.runTool(journalCtx, "bash", map[string]string{"cmd": "git log --oneline -8"})

scripts/evolution/evolve.sh

@@ -176,79 +176,18 @@ log "Generating stats..."
 python3 scripts/build/generate_stats.py . 2>/dev/null || true
 git add docs/stats.json memory/weekly_summary.md 2>/dev/null || true
 
-<<<<<<< Updated upstream
 # ── Final commit and PR ──
 log "Creating pull request..."
 
 BRANCH="evolution/day-${DAY}"
-=======
-# ── Final commit and push ──
-log "Pushing changes..."
-<<<<<<< Updated upstream
-<<<<<<< Updated upstream
->>>>>>> Stashed changes
-=======
->>>>>>> Stashed changes
-=======
->>>>>>> Stashed changes
-
-# Re-calculate day after pull (pull may overwrite DAY_COUNT)
-DAY=$(( ($(date -u +%s) - $(date -d "$BIRTH_DATE" +%s 2>/dev/null || date -j -f "%Y-%m-%d" "$BIRTH_DATE" +%s)) / 86400 ))
-echo "$DAY" > "${REPOPATH}/DAY_COUNT"
-
-<<<<<<< Updated upstream
-<<<<<<< Updated upstream
-<<<<<<< Updated upstream
-# Stage and commit all changes
-=======
->>>>>>> Stashed changes
-=======
->>>>>>> Stashed changes
-=======
->>>>>>> Stashed changes
-if [[ -n $(git status -s) ]]; then
-  git add -A
-  git commit -m "iterate: Day $DAY evolution session" 2>/dev/null || true
-fi
-<<<<<<< Updated upstream
-=======
-git pull --rebase origin main 2>/dev/null || true
-<<<<<<< Updated upstream
-<<<<<<< Updated upstream
-=======
-=======
-
-# Always ensure DAY_COUNT is correct after pull
-echo "$DAY" > "${REPOPATH}/DAY_COUNT"
-git add DAY_COUNT 2>/dev/null || true
-git commit --amend --no-edit 2>/dev/null || git commit -m "iterate: Day $DAY evolution session" 2>/dev/null || true
-
-git push origin main 2>/dev/null || log "Push failed"
->>>>>>> Stashed changes
-
-# Always ensure DAY_COUNT is correct after pull
-echo "$DAY" > "${REPOPATH}/DAY_COUNT"
-git add DAY_COUNT 2>/dev/null || true
-git commit --amend --no-edit 2>/dev/null || git commit -m "iterate: Day $DAY evolution session" 2>/dev/null || true
-
-git push origin main 2>/dev/null || log "Push failed"
->>>>>>> Stashed changes
-
-# Always ensure DAY_COUNT is correct after pull
-echo "$DAY" > "${REPOPATH}/DAY_COUNT"
-git add DAY_COUNT 2>/dev/null || true
-git commit --amend --no-edit 2>/dev/null || git commit -m "iterate: Day $DAY evolution session" 2>/dev/null || true
-
-git push origin main 2>/dev/null || log "Push failed"
->>>>>>> Stashed changes
 
 # Pull latest main
 git pull --rebase origin main 2>/dev/null || true
 
 # Ensure DAY_COUNT is correct after pull
 echo "$DAY" > "${REPOPATH}/DAY_COUNT"
 git add DAY_COUNT 2>/dev/null || true
-git diff --cached --quiet || git commit --amend --no-edit 2>/dev/null || true
+git diff --cached --quiet || git commit -m "chore: update DAY_COUNT to day $DAY" 2>/dev/null || true
 
 # Check if there are changes to push
 if [[ -z $(git diff origin/main HEAD --stat 2>/dev/null) ]]; then
@@ -317,10 +256,15 @@ else
   log "Falling back to direct push to main..."
   git checkout main 2>/dev/null || true
   git pull --rebase origin main 2>/dev/null || true
-  git merge "$BRANCH" --no-edit 2>/dev/null || true
-  git push origin main 2>/dev/null || log "Direct push also failed"
-  git push origin --delete "$BRANCH" 2>/dev/null || true
-  PR_NUMBER=""
+  if ! git merge "$BRANCH" --no-edit 2>/dev/null; then
+    log "ERROR: Merge conflict during fallback — aborting merge, changes remain on $BRANCH"
+    git merge --abort 2>/dev/null || true
+    PR_NUMBER=""
+  else
+    git push origin main 2>/dev/null || log "Direct push also failed"
+    git push origin --delete "$BRANCH" 2>/dev/null || true
+    PR_NUMBER=""
+  fi
 fi
 
 # Get PR number