fix: redirect informational output to stderr in run-filesystem.sh

feat: integrate portable env patching and complete Phase 0.2

feat: implement cross-platform script portability (Phase 0.2)

feat: complete Phase 0.1 - Environment Standardization

git commit -m "feat: standardize environment configuration and enhance startup scripts

docs: add comprehensive implementation plan for MCP Dev Tools

docs: update all documentation for new folder structure

Reorganize repository structure

chore: neutralize personal paths and rename repo-reader -> mcp-dev-tools across docs/scripts

chore(env): document MCP_REF_DIR and .env.local precedence in .env.example

chore(config): update .env.example and .gitignore for .env.local, logs, and temp artifacts

docs: refresh structure, usage, and troubleshooting; note external MCP reference servers and ports/logs

feat(scripts): externalize config, add smoke test, and harden gateways\n\n- Load .env and .env.local in launchers\n- First-run prompt + persistence of REPO_ROOT (start-mcp-dev-tools.sh)\n- start-http.sh reads PORT and wraps stdio via supergateway\n- run-filesystem.sh requires REPO_ROOT and calls reference server\n- start-search.sh loads .env.local and skips when port is occupied\n- health-check.sh verifies ports, logs, and reference server build\n- test-stdio.sh updated initialize test\n- smoke-test.sh automates SSE handshake, initialize, tools/list; fails on error

feat(ops): add start-search.sh (mcp-ripgrep via supergateway), start-all.sh launcher, and .env.example

feat(fs): enforce read-only, deny symlinks, allow-globs; support .env and --port for HTTP proxy