refactor: post-review hardening pass

Independent re-audit surfaced 11 follow-ups across two layers of review
(my fresh-eyes read + a parallel agent pass). Bundled into a single
commit because changes are small and intertwined.

Symlink / state consistency:
- FileSystem.same_symlink now uses raw readlink() instead of resolve().
  Aligns the three sites that ask "is this our link?" (_load_state,
  _check_overwrite_safe, remove_symlink) on a single rule: exact-readlink
  match. Following symlink chains would let externally-modified links
  pass as ours and be silently overwritten.
- LinkedState.from_dict raises ConfigError on missing required fields
  instead of .get(..., False) silent defaults. Matches InstalledState.
- LinkOp.source is now consistently None for remove_link ops; the
  service derives expected_source from current.links. Removes the
  asymmetry between in-state and orphan-broken removal ops.
- _apply_plan: rename shadowing local from link_target to spec.

Fail loud:
- _xdg() now treats XDG_CONFIG_HOME="" the same as unset. Previously
  an empty env var produced Path("") and state files were written to
  $PWD instead of ~/.local/state/flow.
- _resolve_target raises PlanConflict when a package contains a bare
  _root entry (no path components) instead of silently dropping it.
- _strip_prefix raises FlowError when a declared install path does not
  start with its section's expected prefix (e.g. etc/foo under install.bin).

Speculative abstraction removed (CLAUDE.md):
- core.template.substitute (the $VAR form) had no production callers --
  deleted along with its tests; only the {{var}} form remains.
- SetupModule base class -- five subclasses, no shared behaviour, no
  polymorphic call site. Deleted.
- Profile.arch -- parsed but never read. Deleted.
- PackagePlan.pm_command -- set but never read. Deleted (service
  recomputes pm_install_command at the call site).
- FileSystem.ensure_dir(mode=...), .copy_file(sudo=...), .read_text(
  default=...) -- no callers. Deleted along with their test.
- bootstrap _execute_action: the upfront `phase not in VALID_PHASES`
  check duplicated the trailing exhaustive raise. Kept the trailing
  raise as the single source of truth; phase set still documented in
  VALID_PHASES.

Completion ctx threading:
- Removed _config()/_manifest() helpers that re-loaded from disk on
  every completion call. _list_targets, _list_namespaces, _list_platforms,
  _list_bootstrap_profiles, _list_manifest_packages now take ctx and
  read from ctx.config / ctx.manifest.

Test coverage and e2e:
- e2e container test exercises a real `flow dotfiles link` (no dry-run)
  and asserts the resulting symlinks point into the dotfiles dir;
  reruns to verify idempotency.
- New tests: LinkedState corrupt-state ConfigError, LinkedState bad-version
  ConfigError, bare-_root PlanConflict, service-level _root path routing
  + skip semantics.
- 11 stale test imports removed (pyflakes clean across src/ + tests/).

357 unit tests + 1 e2e (gated) all pass.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

tests/test_service_bootstrap.py

@@ -96,21 +96,21 @@ class TestBootstrapService:
 
     def test_unknown_phase_raises(self):
         from flow.domain.bootstrap.models import BootstrapAction, BootstrapPlan
-        from flow.domain.bootstrap.models import VALID_PHASES
 
         manifest = {"profiles": {"work": {"os": "linux"}}}
         ctx = _make_ctx(manifest)
         svc = BootstrapService(ctx)
-        # Forge an action with a phase that VALID_PHASES contains but the
-        # dispatch can't handle (shouldn't happen, but tests the explicit guard).
-        # Use a phase NOT in VALID_PHASES first to confirm the "Unknown" branch.
+        # Forge an action with a phase the dispatcher doesn't handle.
+        # The trailing raise in _execute_action is the single source of
+        # truth for unhandled phases — adding a phase to VALID_PHASES
+        # without a handler should surface here.
         action = BootstrapAction.__new__(BootstrapAction)
         object.__setattr__(action, "phase", "no-such-phase")
         object.__setattr__(action, "description", "")
         object.__setattr__(action, "commands", ())
         object.__setattr__(action, "needs_sudo", False)
         plan = BootstrapPlan(profile="work", actions=(), packages_to_install=())
-        with pytest.raises(FlowError, match="Unknown bootstrap phase"):
+        with pytest.raises(FlowError, match="Unhandled bootstrap phase"):
             svc._execute_action(action, plan, "work")
 
     def test_run_uses_dotfiles_profile_override(self, monkeypatch):