fix(env): seed machine.json so update/mem resolve the real checkout

[mlorentedev]

Problem

On a docs-faithful fresh machine, nothing writes ~/.config/dotfiles/machine.json,
so the phantom contract default DOTFILES_REPO_DIR=$HOME/Projects/dotfiles
propagates through the ADR-025 cascade (env -> machine.json -> contract default) — and through the generated paths.sh/paths.ps1 — into every
consumer that resolves via env.ResolvePath:

• dotf update reports not a git repo: ~/Projects/dotfiles — nothing to self-update and exits 0. Self-deploy is a silent no-op on every fresh machine.
• dotf mem session-start probes ~/Projects/dotfiles/scripts/vault-health.sh,
  misses, and says "run dotfiles setup" though setup ran.

ResolvePath returns the default even when it does not exist, so the
repo == "" guards never fire. Meanwhile secrets/spec/doctor's drift check
use the RepoDir() git walk-up and work — two contradictory "where is the repo"
answers in one binary.

Fix

• Root cause. New dotf env set <KEY> <VALUE> — the write-side counterpart of
  dotf env path: validates the key against the contract (a typo fails loud),
  merges into machine.json preserving every other override, writes atomically.
  setup-linux.sh / setup-windows.ps1 call it to seed DOTFILES_REPO_DIR to
  the checkout they run from, before dotf env generate (so the generated path
  file carries the real value too). One Go JSON-merge instead of hand-rolled JSON
  in two shells (ADR-020).
• Defense in depth. repoForUpdate() and the mem resolvers prefer a
  cascade value only when it names an existing directory, else fall back to the
  RepoDir() walk-up (interactive dotf update/mem from inside a checkout).
• Doctor health check. A new dotf doctor assertion FAILs (with an
  actionable hint) when the DOTFILES_REPO_DIR cascade resolves to a
  phantom/missing path. It deliberately mirrors what update/mem see (no
  walk-up masking), so the class is caught on any box.

Testing

• Go unit tests: env set (merge/preserve/idempotent/unknown-key-fails),
  repoForUpdate walk-up fallback, and the doctor check (pass/missing/not-git).
• End-to-end smoke of dotf env set in an isolated XDG_CONFIG_HOME: seed
  creates machine.json, re-set is idempotent, other keys are preserved, an
  unknown key exits non-zero.
• Integration bats in verify-setup.bats asserts setup seeds machine.json with
  the checkout path and dotf env path DOTFILES_REPO_DIR resolves to a real dir
  (runs in the Linux container).
• go build ./..., go vet ./..., go test ./... clean; bash -n setup-linux.sh; .ps1 change is ASCII-only.

Spec: specs/BUG-029-seed-machine-repo-dir.

Closes #696.

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Review details

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro Plus

Run ID: aa4d44cb-b176-4d62-9123-b4b6c9504eab

📥 Commits

Reviewing files that changed from the base of the PR and between 9be30c7 and c7bff39.

📒 Files selected for processing (15)

• cli/internal/cmd/env.go
• cli/internal/cmd/mem.go
• cli/internal/cmd/update.go
• cli/internal/cmd/update_test.go
• cli/internal/doctor/checks_repodir.go
• cli/internal/doctor/checks_repodir_test.go
• cli/internal/doctor/doctor.go
• cli/internal/env/machine.go
• cli/internal/env/machine_test.go
• setup-linux.sh
• setup-windows.ps1
• specs/BUG-029-seed-machine-repo-dir/proposal.md
• specs/BUG-029-seed-machine-repo-dir/tasks.md
• specs/BUG-029-seed-machine-repo-dir/verification.md
• tests/verify-setup.bats

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch fix/seed-machine-repo-dir

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