refactor: remove mini-swe-agent dependency — inline Docker/Modal backends (#2804)

Drop the mini-swe-agent git submodule. All terminal backends now use
hermes-agent's own environment implementations directly.

Docker backend:
- Inline the `docker run -d` container startup (was 15 lines in
  minisweagent's DockerEnvironment). Our wrapper already handled
  execute(), cleanup(), security hardening, volumes, and resource limits.

Modal backend:
- Import swe-rex's ModalDeployment directly instead of going through
  minisweagent's 90-line passthrough wrapper.
- Bake the _AsyncWorker pattern (from environments/patches.py) directly
  into ModalEnvironment for Atropos compatibility without monkey-patching.

Cleanup:
- Remove minisweagent_path.py (submodule path resolution helper)
- Remove submodule init/install from install.sh and setup-hermes.sh
- Remove mini-swe-agent from .gitmodules
- environments/patches.py is now a no-op (kept for backward compat)
- terminal_tool.py no longer does sys.path hacking for minisweagent
- mini_swe_runner.py guards imports (optional, for RL training only)
- Update all affected tests to mock the new direct subprocess calls
- Update README.md, CONTRIBUTING.md

No functionality change — all Docker, Modal, local, SSH, Singularity,
and Daytona backends behave identically. 6093 tests pass.

scripts/install.sh

@@ -637,13 +637,6 @@ clone_repo() {
 
     cd "$INSTALL_DIR"
 
-    # Only init mini-swe-agent (terminal tool backend — required).
-    # tinker-atropos (RL training) is optional and heavy — users can opt in later
-    # with: git submodule update --init tinker-atropos && uv pip install -e ./tinker-atropos
-    log_info "Initializing mini-swe-agent submodule (terminal backend)..."
-    git submodule update --init mini-swe-agent
-    log_success "Submodule ready"
-
     log_success "Repository ready"
 }
 
@@ -718,18 +711,6 @@ install_deps() {
 
     log_success "Main package installed"
 
-    # Install submodules
-    log_info "Installing mini-swe-agent (terminal tool backend)..."
-    if [ -d "mini-swe-agent" ] && [ -f "mini-swe-agent/pyproject.toml" ]; then
-        if $UV_CMD pip install -e "./mini-swe-agent"; then
-            log_success "mini-swe-agent installed"
-        else
-            log_warn "mini-swe-agent install failed (Docker/Modal terminal backends may not work, local terminal is unaffected)"
-        fi
-    else
-        log_warn "mini-swe-agent not found (run: git submodule update --init)"
-    fi
-
     # tinker-atropos (RL training) is optional — skip by default.
     # To enable RL tools: git submodule update --init tinker-atropos && uv pip install -e "./tinker-atropos"
     if [ -d "tinker-atropos" ] && [ -f "tinker-atropos/pyproject.toml" ]; then