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_domain_dotfiles_resolution.py

@@ -5,7 +5,7 @@ from pathlib import Path
 import pytest
 
 from flow.core.errors import PlanConflict
-from flow.domain.dotfiles.models import LinkTarget, ModuleRef, Package
+from flow.domain.dotfiles.models import ModuleRef, Package
 from flow.domain.dotfiles.resolution import resolve_all_targets, resolve_package_targets
 
 RESERVED_ROOT = "_root"
@@ -56,6 +56,15 @@ class TestResolvePackageTargets:
         targets = resolve_package_targets(pkg, HOME, {"_root"})
         assert len(targets) == 0
 
+    def test_bare_root_marker_raises(self):
+        """A package containing a file literally named `_root` (no children)
+        should be rejected, not silently dropped."""
+        pkg = _pkg("bad", files=[
+            (Path("/dots/_shared/bad/_root"), Path("_root")),
+        ])
+        with pytest.raises(PlanConflict, match="_root"):
+            resolve_package_targets(pkg, HOME, set())
+
     def test_skip_package_by_name(self):
         pkg = _pkg("nvim", files=[
             (Path("/dots/_shared/nvim/.config/nvim/init.lua"), Path(".config/nvim/init.lua")),