from-setup-scripts.md

Migrating from scripts/setup_all.sh

The old scripts still work — they forward to the new entry point and print a deprecation notice. Two behaviours changed, and one of them is deliberate.

Command mapping

Old	New
./scripts/setup_all.sh	./install.sh --profile webui
./scripts/setup_all.sh --check	./install.sh --profile webui --check
./scripts/setup_agent.sh claude	./install.sh configure-agent --agent claude
./scripts/setup_agent.sh cursor	./install.sh configure-agent --agent cursor
./scripts/setup_agent.sh codex	./install.sh configure-agent --agent codex --scope user
./scripts/setup_agent.sh --print-config <a>	./install.sh configure-agent --agent <a> --dry-run
./scripts/setup_agent.sh all	no equivalent — configure each agent you use

New capabilities with no old equivalent:

./install.sh --list                      # compare the three profiles
./install.sh --profile harness           # backend + MCP, no Node.js
./install.sh --profile skills            # skills only, installs no packages
./install.sh --profile webui --dry-run   # show every step, change nothing
./install.sh --uninstall                 # remove what an install recorded

Change 1: installing no longer configures your agent

setup_all.sh ended by running setup_agent.sh all, which wrote ~/.codex/config.toml and ~/.cursor/mcp.json. Installing now writes no agent config at all. Run the configurator yourself:

./install.sh --profile webui
./install.sh configure-agent --agent claude

Reasoning in ADR-003.

Change 2: $HOME needs explicit consent

Agent config defaults to project scope. To write user-level config:

./install.sh configure-agent --agent codex --scope user

It shows a diff and asks before writing. Add --yes to skip the prompt in a script.

setup_agent.sh all is refused rather than silently mapped, because it wrote three config files, two of them in $HOME, without asking.

If the old script already modified your config

Nothing needs undoing. The new configurator is idempotent and merges: it will report "no change" if your existing dataflow entry already matches.

Worth checking once, if you had other MCP servers configured before running the old script — its Cursor path could overwrite ~/.cursor/mcp.json:

cat ~/.cursor/mcp.json      # are your other servers still listed?

If something is missing, re-add it. The new merge path preserves other servers and refuses to touch a file it cannot parse.

AGENTS.md and .cursor/rules/ are now generated

setup_agent.sh regenerated AGENTS.md and .cursor/rules/dataflow-pipeline.mdc. Those are now produced from skills/canonical/ by:

make skills      # = python3 installers/generate_agent_assets.py

They are also no longer tracked in git. .claude/skills/, .cursor/skills/, .codex/skills/, AGENTS.md and the per-skill .cursor/rules/*.mdc are build output now, so a fresh clone will not have them until you run the command above (or ./install.sh, which does it for you). If git status after pulling shows those paths as untracked, that is correct.

AGENTS.md also changed shape: it used to inline every skill's full text (~1100 lines). It is now a routing table that points at .codex/skills/<id>/SKILL.md, so an agent reads only the skill it needs.

Two renamed rules, because rule files now match skill ids:

Old	New
.cursor/rules/dataflow-pipeline.mdc	.cursor/rules/generating-dataflow-pipeline.mdc
.cursor/rules/dataflow-pipeline-generator.mdc	(merged into the above)

Both old files are deleted on regenerate. If you hand-edited either, your changes are gone — move them into skills/canonical/ and regenerate. CI fails on hand-edited generated files.

Hand-written rules with no skill counterpart are untouched: backend-api.mdc, frontend-vue.mdc, dataflow-json-schema.mdc, webui-change-policy.mdc.

Removal timeline

The wrappers are kept for one or two minor releases, then removed. Update your scripts and docs now.