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/e2e/test_dotfiles_e2e.py

@@ -53,6 +53,9 @@ def test_dotfiles_init_and_link_in_container():
         # Run flow inside the container against the mounted example repo.
         # `flow dotfiles init` clones, so we need a real git remote — turn
         # the read-only example mount into a bare-ish working repo first.
+        # --skip system avoids the _root/ paths which would try to sudo-link
+        # over /etc/hostname; we already cover the link path on non-system
+        # packages.
         script = (
             "set -eux; "
             "cp -r /example /home/flowuser/dotfiles-src; "
@@ -62,7 +65,14 @@ def test_dotfiles_init_and_link_in_container():
             "git -c user.email=e2e@example.com -c user.name=e2e commit -q -m initial; "
             "cd /home/flowuser; "
             "flow dotfiles init --repo /home/flowuser/dotfiles-src; "
-            "flow dotfiles link --profile linux-auto --dry-run; "
+            "flow dotfiles link --profile linux-auto --skip system; "
+            # Verify real symlinks were created and point into the dotfiles dir.
+            "test -L /home/flowuser/.zshrc; "
+            "test -L /home/flowuser/.gitconfig; "
+            "readlink /home/flowuser/.zshrc | grep -q '/dotfiles/_shared/zsh/.zshrc'; "
+            "readlink /home/flowuser/.gitconfig | grep -q '/dotfiles/_shared/git/.gitconfig'; "
+            # Idempotency: rerun should be a no-op.
+            "flow dotfiles link --profile linux-auto --skip system; "
             "flow dotfiles status"
         )
         result = subprocess.run(