fix: add git init to 38 Dockerfile.sg_only files + update selection file for SDLC renames

Three fixes in this commit:

1. Add `git init -b main` to 38 Dockerfile.sg_only files that use `COPY repo`
   (not `git clone`). Without git init, the COPY creates a plain directory and
   `git add -A && git commit` fails with exit code 128. This was the root cause
   of all 7 broken MCP reruns (cgen-deps-install-001 + 6 ccb_test tasks).

2. Update selected_benchmark_tasks.json for 4 SDLC suites (debug, design, fix,
   secure = 85 tasks) whose task_dir values referenced old task names from before
   the SDLC phase reorganization. The on-disk directories use new descriptive
   names (e.g., navprove-qb-tab-001 → qutebrowser-tab-regression-prove-001).

3. Add rerun scripts: rerun_7_broken_mcp.sh (MCP-only for git-config-bug tasks)
   and rerun_remaining_suites.sh (4 suites that didn't launch in original batch).

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

Author: sjarmak

benchmarks/ccb_build/bustub-hyperloglog-impl-001/environment/Dockerfile.sg_only

@@ -22,6 +22,6 @@ RUN find /workspace -type f \( -name "*.py" -o -name "*.pyx" -o -name "*.pyi" -o
 # Recommit truncated state so git history cannot recover full files.
 # Without this, `git show HEAD:<file>` or `git checkout HEAD -- <file>`
 # would bypass truncation by reading from the pre-truncation commit.
-RUN cd /workspace && git config user.email "agent@example.com" && git config user.name "Agent" && git add -A && git commit -m "sg_only truncation" --allow-empty --quiet
+RUN cd /workspace && git init -b main && git config user.email "agent@example.com" && git config user.name "Agent" && git add -A && git commit -m "sg_only truncation" --allow-empty --quiet
 RUN touch /tmp/.sg_only_mode && echo '/workspace' > /tmp/.sg_only_workdir
 CMD ["bash"]

benchmarks/ccb_build/cgen-deps-install-001/environment/Dockerfile.sg_only

@@ -22,7 +22,7 @@ RUN find /app/repo -type f \( -name "*.py" -o -name "*.pyx" -o -name "*.pyi" -o
 # Recommit truncated state so git history cannot recover full files.
 # Without this, `git show HEAD:<file>` or `git checkout HEAD -- <file>`
 # would bypass truncation by reading from the pre-truncation commit.
-RUN cd /app/repo && git config user.email "agent@example.com" && git config user.name "Agent" && git add -A && git commit -m "sg_only truncation" --allow-empty --quiet
+RUN cd /app/repo && git init -b main && git config user.email "agent@example.com" && git config user.name "Agent" && git add -A && git commit -m "sg_only truncation" --allow-empty --quiet
 RUN touch /tmp/.sg_only_mode && echo '/app/repo' > /tmp/.sg_only_workdir
 
 WORKDIR /app/repo

benchmarks/ccb_build/codecoverage-deps-install-001/environment/Dockerfile.sg_only

@@ -26,7 +26,7 @@ RUN find /app/repo -type f \( -name "*.py" -o -name "*.pyx" -o -name "*.pyi" -o
 # Recommit truncated state so git history cannot recover full files.
 # Without this, `git show HEAD:<file>` or `git checkout HEAD -- <file>`
 # would bypass truncation by reading from the pre-truncation commit.
-RUN cd /app/repo && git config user.email "agent@example.com" && git config user.name "Agent" && git add -A && git commit -m "sg_only truncation" --allow-empty --quiet
+RUN cd /app/repo && git init -b main && git config user.email "agent@example.com" && git config user.name "Agent" && git add -A && git commit -m "sg_only truncation" --allow-empty --quiet
 RUN touch /tmp/.sg_only_mode && echo '/app/repo' > /tmp/.sg_only_workdir
 
 WORKDIR /app/repo

benchmarks/ccb_build/dotenv-expand-deps-install-001/environment/Dockerfile.sg_only

@@ -24,7 +24,7 @@ RUN find /app/repo -type f \( -name "*.py" -o -name "*.pyx" -o -name "*.pyi" -o
 # Recommit truncated state so git history cannot recover full files.
 # Without this, `git show HEAD:<file>` or `git checkout HEAD -- <file>`
 # would bypass truncation by reading from the pre-truncation commit.
-RUN cd /app/repo && git config user.email "agent@example.com" && git config user.name "Agent" && git add -A && git commit -m "sg_only truncation" --allow-empty --quiet
+RUN cd /app/repo && git init -b main && git config user.email "agent@example.com" && git config user.name "Agent" && git add -A && git commit -m "sg_only truncation" --allow-empty --quiet
 RUN touch /tmp/.sg_only_mode && echo '/app/repo' > /tmp/.sg_only_workdir
 
 WORKDIR /app/repo

benchmarks/ccb_build/dotnetkoans-deps-install-001/environment/Dockerfile.sg_only

@@ -26,7 +26,7 @@ RUN find /app/repo -type f \( -name "*.py" -o -name "*.pyx" -o -name "*.pyi" -o
 # Recommit truncated state so git history cannot recover full files.
 # Without this, `git show HEAD:<file>` or `git checkout HEAD -- <file>`
 # would bypass truncation by reading from the pre-truncation commit.
-RUN cd /app/repo && git config user.email "agent@example.com" && git config user.name "Agent" && git add -A && git commit -m "sg_only truncation" --allow-empty --quiet
+RUN cd /app/repo && git init -b main && git config user.email "agent@example.com" && git config user.name "Agent" && git add -A && git commit -m "sg_only truncation" --allow-empty --quiet
 RUN touch /tmp/.sg_only_mode && echo '/app/repo' > /tmp/.sg_only_workdir
 
 WORKDIR /app/repo

benchmarks/ccb_build/eslint-markdown-deps-install-001/environment/Dockerfile.sg_only

@@ -24,7 +24,7 @@ RUN find /app/repo -type f \( -name "*.py" -o -name "*.pyx" -o -name "*.pyi" -o
 # Recommit truncated state so git history cannot recover full files.
 # Without this, `git show HEAD:<file>` or `git checkout HEAD -- <file>`
 # would bypass truncation by reading from the pre-truncation commit.
-RUN cd /app/repo && git config user.email "agent@example.com" && git config user.name "Agent" && git add -A && git commit -m "sg_only truncation" --allow-empty --quiet
+RUN cd /app/repo && git init -b main && git config user.email "agent@example.com" && git config user.name "Agent" && git add -A && git commit -m "sg_only truncation" --allow-empty --quiet
 RUN touch /tmp/.sg_only_mode && echo '/app/repo' > /tmp/.sg_only_workdir
 
 WORKDIR /app/repo

benchmarks/ccb_build/iamactionhunter-deps-install-001/environment/Dockerfile.sg_only

@@ -22,7 +22,7 @@ RUN find /app/repo -type f \( -name "*.py" -o -name "*.pyx" -o -name "*.pyi" -o
 # Recommit truncated state so git history cannot recover full files.
 # Without this, `git show HEAD:<file>` or `git checkout HEAD -- <file>`
 # would bypass truncation by reading from the pre-truncation commit.
-RUN cd /app/repo && git config user.email "agent@example.com" && git config user.name "Agent" && git add -A && git commit -m "sg_only truncation" --allow-empty --quiet
+RUN cd /app/repo && git init -b main && git config user.email "agent@example.com" && git config user.name "Agent" && git add -A && git commit -m "sg_only truncation" --allow-empty --quiet
 RUN touch /tmp/.sg_only_mode && echo '/app/repo' > /tmp/.sg_only_workdir
 
 WORKDIR /app/repo

benchmarks/ccb_build/pcap-parser-deps-install-001/environment/Dockerfile.sg_only

@@ -24,7 +24,7 @@ RUN find /app/repo -type f \( -name "*.py" -o -name "*.pyx" -o -name "*.pyi" -o
 # Recommit truncated state so git history cannot recover full files.
 # Without this, `git show HEAD:<file>` or `git checkout HEAD -- <file>`
 # would bypass truncation by reading from the pre-truncation commit.
-RUN cd /app/repo && git config user.email "agent@example.com" && git config user.name "Agent" && git add -A && git commit -m "sg_only truncation" --allow-empty --quiet
+RUN cd /app/repo && git init -b main && git config user.email "agent@example.com" && git config user.name "Agent" && git add -A && git commit -m "sg_only truncation" --allow-empty --quiet
 RUN touch /tmp/.sg_only_mode && echo '/app/repo' > /tmp/.sg_only_workdir
 
 WORKDIR /app/repo

benchmarks/ccb_build/python-http-class-naming-refac-001/environment/Dockerfile.sg_only

@@ -11,7 +11,7 @@ RUN find /workspace -type f \( -name "*.py" -o -name "*.pyx" -o -name "*.pyi" -o
 # Recommit truncated state so git history cannot recover full files.
 # Without this, `git show HEAD:<file>` or `git checkout HEAD -- <file>`
 # would bypass truncation by reading from the pre-truncation commit.
-RUN cd /workspace && git config user.email "agent@example.com" && git config user.name "Agent" && git add -A && git commit -m "sg_only truncation" --allow-empty --quiet
+RUN cd /workspace && git init -b main && git config user.email "agent@example.com" && git config user.name "Agent" && git add -A && git commit -m "sg_only truncation" --allow-empty --quiet
 RUN touch /tmp/.sg_only_mode && echo '/workspace' > /tmp/.sg_only_workdir
 
 WORKDIR /workspace

benchmarks/ccb_build/similar-asserts-deps-install-001/environment/Dockerfile.sg_only

@@ -24,7 +24,7 @@ RUN find /app/repo -type f \( -name "*.py" -o -name "*.pyx" -o -name "*.pyi" -o
 # Recommit truncated state so git history cannot recover full files.
 # Without this, `git show HEAD:<file>` or `git checkout HEAD -- <file>`
 # would bypass truncation by reading from the pre-truncation commit.
-RUN cd /app/repo && git config user.email "agent@example.com" && git config user.name "Agent" && git add -A && git commit -m "sg_only truncation" --allow-empty --quiet
+RUN cd /app/repo && git init -b main && git config user.email "agent@example.com" && git config user.name "Agent" && git add -A && git commit -m "sg_only truncation" --allow-empty --quiet
 RUN touch /tmp/.sg_only_mode && echo '/app/repo' > /tmp/.sg_only_workdir
 
 WORKDIR /app/repo