Add optional graphify integration (#49)

[jepegit]

Closes #49.

Summary

Adds an opt-in graphify integration to issue-flow.

• New issue-flow build CLI and /build slash command (with matching /issueflow-build agent skill) wrap the graphify CLI; every extra arg passes through verbatim (--update, --no-viz, --mode deep, --watch, …).
• issue-flow init / update now run graphify cursor install automatically when the graphify CLI is on PATH; otherwise they print install hints and continue. Never blocks.
• The scaffolded rules and /issue-start / /issue-close point agents at graphify-out/GRAPH_REPORT.md when present, so they can navigate by graph instead of grepping. /build is off-path — /iflow never auto-dispatches to it.
• PATH-orphan detection: when graphify is installed but its bin dir isn't on PATH (common after a fresh uv tool install graphifyy without uv tool update-shell and a shell restart), the missing-CLI hint switches to a "found at `` but not on PATH" message that names the directory and tells the user how to fix it.

Install model

Graphify is treated as a separate external CLI, the same way git and gh are:

uv tool install issue-flow
uv tool install graphifyy   # optional; enables /build and graphify cursor install

Initially shipped with a [project.optional-dependencies] graphify = ["graphifyy>=0.7"] extra; this was rolled back before merge because uv tool install only exposes the host package's entry-point scripts on PATH, so an extra (or uv tool install issue-flow --with graphifyy) would have pulled graphifyy in but left the graphify CLI invisible to the shell. The decision is captured in .issueflows/04-designs-and-guides/graphify-integration.md.

Files changed

• src/issue_flow/graphify.py (new) — is_available, register_with_cursor, run_build, find_orphan_install, install-hint printing.
• src/issue_flow/dependencies.py — new RECOMMENDED_DEPENDENCIES list (non-blocking) with the graphify entry, plus check_recommended() helper.
• src/issue_flow/init.py — _graphify_postinstall runs at the end of run_init and run_update.
• src/issue_flow/cli.py — new build Typer command with extra-args passthrough; exits 2 when graphify is missing, propagates graphify's exit code otherwise.
• src/issue_flow/templating.py — manifest gains commands/build.md.j2 and skills/issueflow_build/SKILL.md.j2 (count: 21 → 23).
• New scaffold templates: templates/commands/build.md.j2, templates/skills/issueflow_build/SKILL.md.j2.
• Edits to existing scaffold templates: iflow.md.j2, issue-start.md.j2, issue-close.md.j2, issueflow-rules.mdc.j2, cursor-issue-workflow.md.j2.
• README.md — new "Optional: graphify integration" section, directory listing updated, issue-flow build documented, callouts explaining why a Python extra / --with doesn't work.
• .issueflows/04-designs-and-guides/graphify-integration.md (new) — decision record.
• HISTORY.md — [Unreleased] bullet.

Test plan

• uv run pytest — 100 tests pass (29 new, all hermetic — monkeypatched shutil.which and subprocess.run).
• uv run ruff check src/ tests/ — clean.
• Manual smoke: in a sandbox project, run issue-flow init with and without graphify on PATH; verify .cursor/commands/build.md is written, .cursor/skills/issueflow-build/SKILL.md is written, and graphify cursor install is invoked when graphify is installed.
• Manual smoke: uv tool install graphifyy, ignore the "PATH not set" warning, run issue-flow init, confirm the orphan-detection hint surfaces the actual install path and recommends uv tool update-shell.

Made with Cursor