@ahmed-g-gad/apothem 0.1.1

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Files changed (674) hide show
  1. package/CHANGELOG.md +60 -0
  2. package/LICENSE +21 -0
  3. package/LICENSES/MIT.txt +18 -0
  4. package/LICENSES/PSF-2.0.txt +47 -0
  5. package/README.md +549 -0
  6. package/bin/README.md +37 -0
  7. package/bin/apothem.mjs +78 -0
  8. package/package.json +75 -0
  9. package/pyproject.toml +347 -0
  10. package/src/apothem/README.md +52 -0
  11. package/src/apothem/__init__.py +66 -0
  12. package/src/apothem/__main__.py +28 -0
  13. package/src/apothem/_vendor/.keep +0 -0
  14. package/src/apothem/_vendor/__init__.py +25 -0
  15. package/src/apothem/_vendor/attr/__init__.py +104 -0
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  20. package/src/apothem/_vendor/attr/_config.py +31 -0
  21. package/src/apothem/_vendor/attr/_funcs.py +497 -0
  22. package/src/apothem/_vendor/attr/_make.py +3406 -0
  23. package/src/apothem/_vendor/attr/_next_gen.py +674 -0
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  27. package/src/apothem/_vendor/attr/converters.py +162 -0
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  38. package/src/apothem/_vendor/attr.LICENSE +21 -0
  39. package/src/apothem/_vendor/attrs/__init__.py +72 -0
  40. package/src/apothem/_vendor/attrs/__init__.pyi +314 -0
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  46. package/src/apothem/_vendor/attrs/validators.py +3 -0
  47. package/src/apothem/_vendor/attrs.LICENSE +21 -0
  48. package/src/apothem/_vendor/jsonschema/__init__.py +120 -0
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  67. package/src/apothem/_vendor/jsonschema/benchmarks/useless_keywords.py +32 -0
  68. package/src/apothem/_vendor/jsonschema/benchmarks/validator_creation.py +14 -0
  69. package/src/apothem/_vendor/jsonschema/cli.py +292 -0
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  71. package/src/apothem/_vendor/jsonschema/protocols.py +230 -0
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  76. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft201909/metaschema.json +42 -0
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  90. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft202012/vocabularies/unevaluated +15 -0
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  92. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft3/metaschema.json +172 -0
  93. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft4/metaschema.json +149 -0
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  95. package/src/apothem/_vendor/jsonschema_specifications/schemas/draft7/metaschema.json +166 -0
  96. package/src/apothem/_vendor/jsonschema_specifications.LICENSE +19 -0
  97. package/src/apothem/_vendor/referencing/__init__.py +7 -0
  98. package/src/apothem/_vendor/referencing/_attrs.py +31 -0
  99. package/src/apothem/_vendor/referencing/_attrs.pyi +21 -0
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  103. package/src/apothem/_vendor/referencing/py.typed +0 -0
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  105. package/src/apothem/_vendor/referencing/typing.py +61 -0
  106. package/src/apothem/_vendor/referencing.LICENSE +19 -0
  107. package/src/apothem/_vendor/rpds/__init__.py +251 -0
  108. package/src/apothem/_vendor/typing_extensions.LICENSE +279 -0
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  116. package/src/apothem/_vendor/yaml/emitter.py +1137 -0
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  126. package/src/apothem/_vendor/yaml/serializer.py +110 -0
  127. package/src/apothem/_vendor/yaml/tokens.py +103 -0
  128. package/src/apothem/_vendor/yaml.LICENSE +20 -0
  129. package/src/apothem/agents/README.md +60 -0
  130. package/src/apothem/agents/codebase-explorer.md +91 -0
  131. package/src/apothem/agents/convention-auditor.md +93 -0
  132. package/src/apothem/agents/dependency-auditor.md +97 -0
  133. package/src/apothem/agents/fact-checker.md +84 -0
  134. package/src/apothem/agents/mcp-builder.md +86 -0
  135. package/src/apothem/agents/memory-auditor.md +93 -0
  136. package/src/apothem/agents/prompt-evaluator.md +87 -0
  137. package/src/apothem/agents/quality-gate.md +103 -0
  138. package/src/apothem/agents/refactor-surgeon.md +74 -0
  139. package/src/apothem/agents/research-scout.md +73 -0
  140. package/src/apothem/agents/security-scanner.md +83 -0
  141. package/src/apothem/agents/test-runner.md +84 -0
  142. package/src/apothem/audit/README.md +73 -0
  143. package/src/apothem/audit/_scan_lib.py +182 -0
  144. package/src/apothem/audit/analyze_graph.py +260 -0
  145. package/src/apothem/audit/build_capability_graph.py +607 -0
  146. package/src/apothem/audit/build_inventory.py +657 -0
  147. package/src/apothem/audit/build_plans_provenance.py +997 -0
  148. package/src/apothem/audit/check_links.py +389 -0
  149. package/src/apothem/audit/classify_artifacts.py +381 -0
  150. package/src/apothem/audit/deprecated-tokens.txt +10 -0
  151. package/src/apothem/audit/execute_plans_migration.py +491 -0
  152. package/src/apothem/audit/known-projects.txt +15 -0
  153. package/src/apothem/audit/render_capability_index.py +467 -0
  154. package/src/apothem/audit/render_inventory.py +405 -0
  155. package/src/apothem/audit/scan_ai_surfaces.py +1125 -0
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  194. package/src/apothem/cli/reference_export.py +126 -0
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  585. package/src/apothem/rules/planning-techniques.md +130 -0
  586. package/src/apothem/rules/pre-emission-gate-bars.md +86 -0
  587. package/src/apothem/rules/pre-emission-gate.md +54 -0
  588. package/src/apothem/rules/production-ready-prs-surfaces.md +162 -0
  589. package/src/apothem/rules/production-ready-prs.md +83 -0
  590. package/src/apothem/rules/propagation.md +63 -0
  591. package/src/apothem/rules/recommend-next-step.md +106 -0
  592. package/src/apothem/rules/refactoring-discipline.md +76 -0
  593. package/src/apothem/rules/session-closure.md +44 -0
  594. package/src/apothem/rules/sota-elevation-exemplars.md +76 -0
  595. package/src/apothem/rules/sota-elevation.md +52 -0
  596. package/src/apothem/rules/source-accessibility.md +58 -0
  597. package/src/apothem/rules/surgical-manipulation.md +48 -0
  598. package/src/apothem/rules/systemic-participation-relations.md +108 -0
  599. package/src/apothem/rules/systemic-participation.md +70 -0
  600. package/src/apothem/rules/ten-dimension-check-dimensions.md +52 -0
  601. package/src/apothem/rules/ten-dimension-check.md +59 -0
  602. package/src/apothem/rules/token-budget-discipline.md +81 -0
  603. package/src/apothem/rules/token-efficiency-rewrite-protocol.md +79 -0
  604. package/src/apothem/rules/token-efficiency-rewrite.md +77 -0
  605. package/src/apothem/rules/tool-use-discipline.md +48 -0
  606. package/src/apothem/rules/visual-leverage.md +102 -0
  607. package/src/apothem/schemas/NOTICE.md +9 -0
  608. package/src/apothem/schemas/README.md +104 -0
  609. package/src/apothem/schemas/__init__.py +176 -0
  610. package/src/apothem/schemas/advisory-finding.schema.json +111 -0
  611. package/src/apothem/schemas/agent.schema.json +106 -0
  612. package/src/apothem/schemas/authorship-header.txt +1 -0
  613. package/src/apothem/schemas/cohort-manifest.yaml +248 -0
  614. package/src/apothem/schemas/cohort-metadata-vocabulary.yaml +168 -0
  615. package/src/apothem/schemas/cohort.schema.json +113 -0
  616. package/src/apothem/schemas/command.schema.json +68 -0
  617. package/src/apothem/schemas/compatibility-matrix.yaml +432 -0
  618. package/src/apothem/schemas/context-fragment.schema.json +64 -0
  619. package/src/apothem/schemas/freshness-token-denylist.txt +51 -0
  620. package/src/apothem/schemas/handoff-manifest.yaml +353 -0
  621. package/src/apothem/schemas/header-exceptions.txt +141 -0
  622. package/src/apothem/schemas/header-visibility.yaml +39 -0
  623. package/src/apothem/schemas/learning-signal.schema.json +46 -0
  624. package/src/apothem/schemas/memory-record.schema.json +61 -0
  625. package/src/apothem/schemas/output-style.schema.json +40 -0
  626. package/src/apothem/schemas/plan.schema.json +51 -0
  627. package/src/apothem/schemas/plugin.schema.json +83 -0
  628. package/src/apothem/schemas/profile.example.yaml +70 -0
  629. package/src/apothem/schemas/profile.minimal.yaml +6 -0
  630. package/src/apothem/schemas/profile.schema.json +396 -0
  631. package/src/apothem/schemas/reference-token-denylist.txt +25 -0
  632. package/src/apothem/schemas/skill.schema.json +75 -0
  633. package/src/apothem/skills/README.md +93 -0
  634. package/src/apothem/skills/dependency-upgrade/SKILL.md +105 -0
  635. package/src/apothem/skills/dev-toolkit/SKILL.md +120 -0
  636. package/src/apothem/skills/diagram-authoring/SKILL.md +113 -0
  637. package/src/apothem/skills/document-authoring/SKILL.md +118 -0
  638. package/src/apothem/skills/ecosystem-audit/SKILL.md +108 -0
  639. package/src/apothem/skills/ecosystem-audit/references/audit-fortress.md +85 -0
  640. package/src/apothem/skills/ecosystem-audit/references/procedure.md +162 -0
  641. package/src/apothem/skills/eval-harness/SKILL.md +88 -0
  642. package/src/apothem/skills/incident-runbook/SKILL.md +92 -0
  643. package/src/apothem/skills/multi-source-research/SKILL.md +90 -0
  644. package/src/apothem/skills/plan-suite/SKILL.md +118 -0
  645. package/src/apothem/skills/plan-suite/master_template.md +1324 -0
  646. package/src/apothem/skills/projectify/SKILL.md +117 -0
  647. package/src/apothem/skills/prompt-engineering/SKILL.md +122 -0
  648. package/src/apothem/skills/refactor-extract/SKILL.md +85 -0
  649. package/src/apothem/skills/research-suite/SKILL.md +170 -0
  650. package/src/apothem/skills/research-suite/references/directory-structure.md +47 -0
  651. package/src/apothem/skills/research-suite/references/lifecycle.md +67 -0
  652. package/src/apothem/skills/research-suite/references/principal-investigator-framework.md +37 -0
  653. package/src/apothem/skills/research-suite/references/rigor-mandates.md +30 -0
  654. package/src/apothem/skills/research-suite/research_template.md +476 -0
  655. package/src/apothem/skills/secret-rotation/SKILL.md +87 -0
  656. package/src/apothem/skills/source-synthesis/SKILL.md +92 -0
  657. package/src/apothem/skills/surgical-guard/SKILL.md +118 -0
  658. package/src/apothem/skills/test-authoring/SKILL.md +85 -0
  659. package/src/apothem/skills/vuln-triage/SKILL.md +91 -0
  660. package/src/apothem/skills/workflow/SKILL.md +139 -0
  661. package/src/apothem/statuslines/README.md +26 -0
  662. package/src/apothem/statuslines/__init__.py +20 -0
  663. package/src/apothem/statuslines/conformity.json +5 -0
  664. package/src/apothem/statuslines/render.py +334 -0
  665. package/src/apothem/statuslines/statusline.md +50 -0
  666. package/src/apothem/templates/README.md +43 -0
  667. package/src/apothem/templates/agents-md-template.md +80 -0
  668. package/src/apothem/templates/consideration-log.md +39 -0
  669. package/src/apothem/templates/expertise-gap-log.md +56 -0
  670. package/src/apothem/templates/master-index-template.md +93 -0
  671. package/src/apothem/templates/potency-map.md +53 -0
  672. package/src/apothem/templates/preservation-audit.md +60 -0
  673. package/src/apothem/templates/question-resolution-audit.md +52 -0
  674. package/src/apothem/templates/trace-matrix-template.md +77 -0
@@ -0,0 +1,396 @@
1
+ # SPDX-License-Identifier: MIT
2
+
3
+ """Clean-slate installer routine: bounded, backed-up, opt-in target removal.
4
+
5
+ This module is the engine-side single source of truth for the opt-in
6
+ destructive install path. It owns the safety contract end to end: a closed
7
+ removal target set, an unsafe-root guard, a timestamped backup taken before
8
+ any removal, per-target confirmation, a dry-run preview, and a non-interactive
9
+ override that must be requested explicitly.
10
+
11
+ The shell installers forward to ``apothem install --clean``; the CLI handler
12
+ calls :func:`run_clean_slate` directly. The routine never reads global process
13
+ state for its target home — the caller passes ``home`` explicitly — so it is
14
+ fully exercisable against a sandbox directory without ever touching a real
15
+ home directory.
16
+
17
+ The closed removal target set is the four paths under the resolved home:
18
+ ``~/.claude``, ``~/.codex``, ``~/.agents``, and ``~/.config/apothem``. Every
19
+ other ``~/.config`` entry is preserved; the entire ``~/.config`` directory is
20
+ never a removal target.
21
+ """
22
+
23
+ from __future__ import annotations
24
+
25
+ import shutil
26
+ import stat
27
+ from collections.abc import Callable, Sequence
28
+ from dataclasses import dataclass
29
+ from datetime import datetime, timezone
30
+ from pathlib import Path
31
+
32
+ __all__ = [
33
+ "BackupError",
34
+ "CleanSlateError",
35
+ "CleanSlateResult",
36
+ "Clock",
37
+ "ConfirmFn",
38
+ "EchoFn",
39
+ "TargetDisposition",
40
+ "UnsafeRootError",
41
+ "bounded_targets",
42
+ "run_clean_slate",
43
+ ]
44
+
45
+ # The closed removal target set: exactly these paths under the resolved home
46
+ # directory, and nothing else. Extending the set is a code change, never a
47
+ # runtime argument.
48
+ _BOUNDED_TARGET_RELPATHS: tuple[tuple[str, ...], ...] = (
49
+ (".claude",),
50
+ (".codex",),
51
+ (".agents",),
52
+ (".config", "apothem"),
53
+ )
54
+
55
+ # The only entry removable directly under ``~/.config``; every other child of
56
+ # ``~/.config`` is preserved.
57
+ _CONFIG_DIRNAME = ".config"
58
+ _CONFIG_REMOVABLE_CHILD = "apothem"
59
+
60
+ #: A predicate that decides whether a single target should be removed.
61
+ ConfirmFn = Callable[[Path], bool]
62
+ #: A source of the current time, injected so backups are deterministic in tests.
63
+ Clock = Callable[[], datetime]
64
+ #: A sink for human-facing progress lines.
65
+ EchoFn = Callable[[str], None]
66
+
67
+
68
+ class CleanSlateError(RuntimeError):
69
+ """Base error for the clean-slate routine."""
70
+
71
+
72
+ class UnsafeRootError(CleanSlateError):
73
+ """Raised when a removal target resolves to an unsafe root.
74
+
75
+ The guard refuses the home directory itself, a filesystem or drive root,
76
+ an empty or unset path, the entire ``~/.config`` directory, and any
77
+ ``~/.config`` child other than ``apothem``.
78
+ """
79
+
80
+
81
+ class BackupError(CleanSlateError):
82
+ """Raised when the pre-removal backup cannot be written.
83
+
84
+ When this is raised no target has been removed: the backup precedes every
85
+ removal, and a backup failure aborts the run.
86
+ """
87
+
88
+
89
+ @dataclass(frozen=True)
90
+ class TargetDisposition:
91
+ """The outcome for a single removal target.
92
+
93
+ Attributes:
94
+ path: The resolved target path.
95
+ present: Whether the target existed on disk when the run began.
96
+ removed: Whether the target was removed during this run.
97
+ skipped_reason: Why a present target was not removed, when applicable
98
+ (for example, ``"declined"`` when per-target confirmation was
99
+ answered in the negative).
100
+ """
101
+
102
+ path: Path
103
+ present: bool
104
+ removed: bool = False
105
+ skipped_reason: str | None = None
106
+
107
+
108
+ @dataclass(frozen=True)
109
+ class CleanSlateResult:
110
+ """The aggregate outcome of a clean-slate run.
111
+
112
+ Attributes:
113
+ dry_run: Whether the run was a preview that changed nothing on disk.
114
+ backup_dir: The timestamped backup directory, or ``None`` when no
115
+ present target required backing up (or in a dry run).
116
+ dispositions: The per-target outcome, one entry per bounded target.
117
+ """
118
+
119
+ dry_run: bool
120
+ backup_dir: Path | None
121
+ dispositions: tuple[TargetDisposition, ...]
122
+
123
+ @property
124
+ def removed(self) -> tuple[Path, ...]:
125
+ """The targets removed during this run."""
126
+ return tuple(d.path for d in self.dispositions if d.removed)
127
+
128
+ @property
129
+ def present_targets(self) -> tuple[Path, ...]:
130
+ """The targets that existed on disk when the run began."""
131
+ return tuple(d.path for d in self.dispositions if d.present)
132
+
133
+
134
+ def bounded_targets(home: Path) -> list[Path]:
135
+ """Return the closed removal target set under ``home``.
136
+
137
+ Args:
138
+ home: The resolved home directory the targets are relative to.
139
+
140
+ Returns:
141
+ Exactly four paths — ``~/.claude``, ``~/.codex``, ``~/.agents``, and
142
+ ``~/.config/apothem`` — in that order, and nothing else.
143
+ """
144
+ return [home.joinpath(*parts) for parts in _BOUNDED_TARGET_RELPATHS]
145
+
146
+
147
+ def _unsafe_reason(target: Path, home: Path) -> str | None:
148
+ """Return a refusal reason for an unsafe target, or ``None`` when safe."""
149
+ if not str(target).strip():
150
+ return "refuses empty or unset path"
151
+ resolved = target.expanduser()
152
+ # Reject any parent-directory traversal before the equality checks below:
153
+ # those checks compare the unresolved path, so a ".."-bearing target (e.g.
154
+ # ~/x/.. resolving to the home directory, or ~/.claude/../.. climbing above
155
+ # it) would otherwise slip past them and be removed. Rejecting ".." outright
156
+ # — rather than canonicalizing with resolve() — also preserves the
157
+ # deliberate do-not-follow-symlinks contract this routine upholds.
158
+ if ".." in resolved.parts:
159
+ return f"refuses parent-directory traversal: {resolved}"
160
+ if resolved == Path(resolved.anchor) or resolved.parent == resolved:
161
+ return f"refuses filesystem root: {resolved}"
162
+ if resolved == home:
163
+ return f"refuses home directory itself: {resolved}"
164
+ config_dir = home / _CONFIG_DIRNAME
165
+ if resolved == config_dir:
166
+ return f"refuses entire {config_dir} (would remove unrelated applications)"
167
+ if resolved.parent == config_dir and resolved.name != _CONFIG_REMOVABLE_CHILD:
168
+ return f"refuses non-apothem ~/.config entry: {resolved}"
169
+ return None
170
+
171
+
172
+ def _utcnow() -> datetime:
173
+ """Return the current UTC time."""
174
+ return datetime.now(timezone.utc)
175
+
176
+
177
+ def _timestamp(clock: Clock) -> str:
178
+ """Render an ISO-8601 basic-format UTC timestamp for backup directories."""
179
+ return clock().strftime("%Y%m%dT%H%M%SZ")
180
+
181
+
182
+ def _exists(path: Path) -> bool:
183
+ """Return whether a path exists, counting broken symlinks as present."""
184
+ return path.exists() or path.is_symlink()
185
+
186
+
187
+ def _backup_targets(
188
+ present: Sequence[Path],
189
+ backup_root: Path,
190
+ home: Path,
191
+ clock: Clock,
192
+ ) -> Path:
193
+ """Copy every present target into a fresh timestamped backup directory.
194
+
195
+ Args:
196
+ present: The targets that exist on disk and must be backed up.
197
+ backup_root: The directory the timestamped backup is created under.
198
+ home: The resolved home directory, used to preserve relative layout.
199
+ clock: The time source for the timestamp.
200
+
201
+ Returns:
202
+ The created backup directory.
203
+
204
+ Raises:
205
+ BackupError: When any part of the backup cannot be written. No target
206
+ is removed when this is raised.
207
+ """
208
+ backup_dir = backup_root / f"clean-slate-{_timestamp(clock)}"
209
+ try:
210
+ backup_dir.mkdir(parents=True, exist_ok=True)
211
+ for src in present:
212
+ try:
213
+ rel: Path = src.relative_to(home)
214
+ except ValueError:
215
+ rel = Path(src.name)
216
+ dest = backup_dir / rel
217
+ dest.parent.mkdir(parents=True, exist_ok=True)
218
+ if src.is_dir() and not src.is_symlink():
219
+ shutil.copytree(src, dest, symlinks=True, dirs_exist_ok=True)
220
+ else:
221
+ shutil.copy2(src, dest, follow_symlinks=False)
222
+ except OSError as exc:
223
+ raise BackupError(f"backup write failed under {backup_dir}: {exc}") from exc
224
+ return backup_dir
225
+
226
+
227
+ def _remove_tree(path: Path) -> None:
228
+ """Remove a directory tree, clearing read-only bits on a first failure.
229
+
230
+ The retry clears the read-only attribute that Windows sets on some files
231
+ (for example, files under a ``.git`` object store) and which otherwise
232
+ blocks removal.
233
+ """
234
+ try:
235
+ shutil.rmtree(path)
236
+ except OSError:
237
+ for child in sorted(path.rglob("*"), reverse=True):
238
+ try:
239
+ child.chmod(stat.S_IWRITE)
240
+ if child.is_dir() and not child.is_symlink():
241
+ child.rmdir()
242
+ else:
243
+ child.unlink(missing_ok=True)
244
+ except OSError:
245
+ continue
246
+ path.chmod(stat.S_IWRITE)
247
+ shutil.rmtree(path)
248
+
249
+
250
+ def _remove_path(path: Path) -> None:
251
+ """Remove a single target, whether a symlink, directory, or file."""
252
+ if path.is_symlink():
253
+ path.unlink(missing_ok=True)
254
+ elif path.is_dir():
255
+ _remove_tree(path)
256
+ else:
257
+ path.unlink(missing_ok=True)
258
+
259
+
260
+ def _default_confirm(path: Path) -> bool:
261
+ """Prompt interactively for confirmation to remove a single target."""
262
+ try:
263
+ reply = input(f"Remove {path}? [y/N] ").strip().lower()
264
+ except EOFError:
265
+ return False
266
+ return reply in {"y", "yes"}
267
+
268
+
269
+ def run_clean_slate(
270
+ home: Path,
271
+ *,
272
+ dry_run: bool = False,
273
+ assume_yes: bool = False,
274
+ interactive: bool = True,
275
+ confirm: ConfirmFn | None = None,
276
+ targets: Sequence[Path] | None = None,
277
+ backup_root: Path | None = None,
278
+ clock: Clock | None = None,
279
+ echo: EchoFn | None = None,
280
+ ) -> CleanSlateResult:
281
+ """Run the opt-in clean-slate removal with the full safety contract.
282
+
283
+ The ordering is fixed: guard, then (for a real run) back up every present
284
+ target, then confirm and remove each target individually. A dry run reports
285
+ the disposition of every target and changes nothing on disk.
286
+
287
+ Args:
288
+ home: The resolved home directory the bounded target set is relative
289
+ to. Passed explicitly so the routine is sandbox-testable.
290
+ dry_run: When true, preview the disposition of every target and change
291
+ nothing on disk.
292
+ assume_yes: When true, bypass per-target confirmation (the
293
+ non-interactive opt-in).
294
+ interactive: Whether the caller is attached to an interactive terminal.
295
+ When false and ``assume_yes`` is not set, the run refuses rather
296
+ than auto-confirming.
297
+ confirm: A per-target confirmation predicate. Defaults to an
298
+ interactive prompt.
299
+ targets: An explicit target list, defaulting to :func:`bounded_targets`.
300
+ Provided for tests; production callers use the default.
301
+ backup_root: The directory backups are written under. Defaults to
302
+ ``~/.apothem/backups``, which lies outside the bounded target set.
303
+ clock: The time source for the backup timestamp.
304
+ echo: A sink for human-facing progress lines.
305
+
306
+ Returns:
307
+ A :class:`CleanSlateResult` describing the disposition of every target.
308
+
309
+ Raises:
310
+ UnsafeRootError: When the home directory or any target is unsafe.
311
+ CleanSlateError: When the run is non-interactive without ``assume_yes``.
312
+ BackupError: When the pre-removal backup cannot be written.
313
+ """
314
+ emit: EchoFn = echo if echo is not None else (lambda _message: None)
315
+ tick: Clock = clock if clock is not None else _utcnow
316
+
317
+ if not str(home).strip():
318
+ raise UnsafeRootError("refuses empty or unset home directory")
319
+ home_resolved = home.expanduser()
320
+ if (
321
+ home_resolved == Path(home_resolved.anchor)
322
+ or home_resolved.parent == home_resolved
323
+ ):
324
+ raise UnsafeRootError(f"refuses filesystem root as home: {home_resolved}")
325
+
326
+ target_list = (
327
+ [t.expanduser() for t in targets]
328
+ if targets is not None
329
+ else bounded_targets(home_resolved)
330
+ )
331
+
332
+ # Unsafe-root guard over every target — refuse before any backup or removal.
333
+ for target in target_list:
334
+ reason = _unsafe_reason(target, home_resolved)
335
+ if reason is not None:
336
+ raise UnsafeRootError(reason)
337
+
338
+ if dry_run:
339
+ emit("Clean-slate dry-run — no files will be changed.")
340
+ dispositions = tuple(
341
+ TargetDisposition(path=target, present=_exists(target))
342
+ for target in target_list
343
+ )
344
+ for disposition in dispositions:
345
+ verb = "remove" if disposition.present else "absent"
346
+ emit(f" {verb}: {disposition.path}")
347
+ return CleanSlateResult(
348
+ dry_run=True, backup_dir=None, dispositions=dispositions
349
+ )
350
+
351
+ if not interactive and not assume_yes:
352
+ raise CleanSlateError(
353
+ "refusing destructive clean-slate in a non-interactive context "
354
+ "without an explicit confirmation flag",
355
+ )
356
+
357
+ present = [target for target in target_list if _exists(target)]
358
+
359
+ backup_dir: Path | None = None
360
+ if present:
361
+ root = (
362
+ backup_root
363
+ if backup_root is not None
364
+ else home_resolved / ".apothem" / "backups"
365
+ )
366
+ backup_dir = _backup_targets(present, root, home_resolved, tick)
367
+ emit(f"Backed up {len(present)} target(s) to {backup_dir}")
368
+
369
+ confirm_fn: ConfirmFn = confirm if confirm is not None else _default_confirm
370
+ dispositions_built: list[TargetDisposition] = []
371
+ for target in target_list:
372
+ if not _exists(target):
373
+ dispositions_built.append(TargetDisposition(path=target, present=False))
374
+ continue
375
+ if not assume_yes and not confirm_fn(target):
376
+ dispositions_built.append(
377
+ TargetDisposition(
378
+ path=target,
379
+ present=True,
380
+ removed=False,
381
+ skipped_reason="declined",
382
+ )
383
+ )
384
+ emit(f" skipped (declined): {target}")
385
+ continue
386
+ _remove_path(target)
387
+ dispositions_built.append(
388
+ TargetDisposition(path=target, present=True, removed=True)
389
+ )
390
+ emit(f" removed: {target}")
391
+
392
+ return CleanSlateResult(
393
+ dry_run=False,
394
+ backup_dir=backup_dir,
395
+ dispositions=tuple(dispositions_built),
396
+ )