@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 +1,495 @@
1
+ # SPDX-License-Identifier: MIT
2
+
3
+ """Uninstall, verify, fidelity, and the pure build_plan entrypoint."""
4
+
5
+ from __future__ import annotations
6
+
7
+ import json
8
+ import shutil
9
+ from dataclasses import dataclass
10
+ from pathlib import Path
11
+ from typing import Any, Literal
12
+
13
+ import yaml
14
+
15
+ from apothem.harnesses._shared import install_driver
16
+ from apothem.lib import install_ledger
17
+ from apothem.lib.data_home import resolve_shared_data_home
18
+ from apothem.lib.harness_materializer import (
19
+ extract_managed_block,
20
+ )
21
+ from apothem.lib.harness_registry import SUPPORTED_HARNESS_IDS
22
+ from apothem.lib.install_ledger import LedgerRecord
23
+ from apothem.lib.propagation import (
24
+ InstallEntry,
25
+ resolve_target,
26
+ )
27
+
28
+ from .install_driver_backup import _replace_path, backup_existing
29
+ from .install_driver_merge import render_content_tokens
30
+ from .install_driver_pathsafety import (
31
+ _allowed_write_root,
32
+ _root_for,
33
+ _validate_target_path,
34
+ )
35
+ from .install_driver_planvalidation import (
36
+ _generated_targets_for_entry,
37
+ _projected_profile_body,
38
+ )
39
+ from .install_driver_removal import _surgical_remove_from_target
40
+ from .install_driver_types import (
41
+ MaterializationResult,
42
+ _handle_rm_error,
43
+ _path_text,
44
+ _result,
45
+ resolve_source,
46
+ )
47
+
48
+
49
+ def _native_config_parses(target: Path) -> bool:
50
+ """Return True unless *target* is a structurally invalid JSON/YAML file.
51
+
52
+ Only ``.json``/``.yaml``/``.yml`` targets are parsed; other suffixes (e.g.
53
+ Markdown anchors) pass trivially. A present-but-corrupt config reads as
54
+ not-installed.
55
+ """
56
+ suffix = target.suffix.lower()
57
+ if suffix not in {".json", ".yaml", ".yml"}:
58
+ return True
59
+ try:
60
+ text = target.read_text(encoding="utf-8")
61
+ except OSError:
62
+ return False
63
+ try:
64
+ if suffix == ".json":
65
+ json.loads(text)
66
+ else:
67
+ yaml.safe_load(text)
68
+ except (json.JSONDecodeError, yaml.YAMLError):
69
+ return False
70
+ return True
71
+
72
+
73
+ def verify_install(
74
+ harness_name: str,
75
+ *,
76
+ harness_root: Path | None = None,
77
+ project_root: Path | None = None,
78
+ native_config: Path | None = None,
79
+ ) -> bool:
80
+ """Return True when every manifest install-list target is present + valid.
81
+
82
+ Walks the harness's manifest install list and resolves each target against
83
+ the supplied root: ``write_text``/``sentinel_merge`` targets must be
84
+ non-empty regular files, ``replace_tree`` targets must be directories, and
85
+ every other mode (tree merges, cohort conversions) must exist. JSON/YAML
86
+ config targets are additionally parsed — a corrupt config reads as
87
+ not-installed. *native_config* (the adapter's dynamically-rendered config
88
+ file, which is not a manifest entry) is checked the same way when supplied.
89
+ Returns False on the first unsatisfied target.
90
+ """
91
+ rules = install_driver.load_rules(harness_name)
92
+ if native_config is not None:
93
+ if not native_config.is_file() or native_config.stat().st_size <= 0:
94
+ return False
95
+ if not _native_config_parses(native_config):
96
+ return False
97
+ for entry in rules.install:
98
+ target = resolve_target(
99
+ entry.target, harness_root=harness_root, project_root=project_root
100
+ )
101
+ if entry.mode in {"write_text", "sentinel_merge"}:
102
+ if not target.is_file() or target.stat().st_size <= 0:
103
+ return False
104
+ if not _native_config_parses(target):
105
+ return False
106
+ elif entry.mode == "replace_tree":
107
+ if not target.is_dir():
108
+ return False
109
+ elif not target.exists():
110
+ return False
111
+ return True
112
+
113
+
114
+ @dataclass(frozen=True)
115
+ class FidelityResult:
116
+ """The drift verdict for one profile-derived anchor on disk."""
117
+
118
+ target: str
119
+ status: Literal["faithful", "drifted", "missing"]
120
+
121
+
122
+ def _profile_anchor_targets(
123
+ harness_name: str,
124
+ *,
125
+ harness_root: Path | None,
126
+ project_root: Path | None,
127
+ ) -> list[Path]:
128
+ """Return the on-disk anchors that carry the projected profile managed block.
129
+
130
+ Every ``sentinel_merge`` manifest target (anchor adapters fold the projected
131
+ body into these), plus the two bolt-on profile anchors written outside the
132
+ manifest when present: claude_code's ``CLAUDE.md`` and the single-file-config
133
+ adapters' ``apothem/rules/00-apothem-profile.md``.
134
+ """
135
+ rules = install_driver.load_rules(harness_name)
136
+ root = _root_for(harness_root, project_root)
137
+ targets: list[Path] = [
138
+ resolve_target(
139
+ entry.target, harness_root=harness_root, project_root=project_root
140
+ )
141
+ for entry in rules.install
142
+ if entry.mode == "sentinel_merge"
143
+ ]
144
+ for relative in ("CLAUDE.md", "apothem/rules/00-apothem-profile.md"):
145
+ bolt_on = root / relative
146
+ if bolt_on.is_file():
147
+ targets.append(bolt_on)
148
+ return targets
149
+
150
+
151
+ def check_fidelity(
152
+ harness_name: str,
153
+ *,
154
+ harness_root: Path | None = None,
155
+ project_root: Path | None = None,
156
+ profile: dict[str, Any],
157
+ ) -> list[FidelityResult]:
158
+ """Classify each profile-derived anchor as faithful / drifted / missing.
159
+
160
+ Re-projects *profile* through the same seam ``run_install`` uses and requires
161
+ the freshly-projected managed-block body to appear verbatim inside the
162
+ on-disk anchor's managed block. An anchor whose projected content was edited
163
+ on disk (so the freshly-projected body is no longer a substring) reads as
164
+ ``drifted``; an absent anchor or one with no managed block reads as
165
+ ``missing``; an exact carry reads as ``faithful``. This is what makes the CLI
166
+ ``verify`` answer "is the profile faithfully installed?" rather than merely
167
+ "does a file exist".
168
+ """
169
+ expected = _projected_profile_body(harness_name, profile) or ""
170
+ results: list[FidelityResult] = []
171
+ for target in _profile_anchor_targets(
172
+ harness_name, harness_root=harness_root, project_root=project_root
173
+ ):
174
+ if not target.is_file():
175
+ results.append(FidelityResult(_path_text(target), "missing"))
176
+ continue
177
+ try:
178
+ text = target.read_text(encoding="utf-8")
179
+ except OSError:
180
+ results.append(FidelityResult(_path_text(target), "missing"))
181
+ continue
182
+ block = extract_managed_block(text)
183
+ if block is None:
184
+ results.append(FidelityResult(_path_text(target), "missing"))
185
+ elif expected and expected in block:
186
+ results.append(FidelityResult(_path_text(target), "faithful"))
187
+ else:
188
+ results.append(FidelityResult(_path_text(target), "drifted"))
189
+ return results
190
+
191
+
192
+ def fidelity_is_faithful(results: list[FidelityResult]) -> bool:
193
+ """Reduce per-anchor fidelity results to a single bool (all faithful)."""
194
+ return bool(results) and all(result.status == "faithful" for result in results)
195
+
196
+
197
+ def _rendered_template_text(
198
+ entry: InstallEntry,
199
+ *,
200
+ harness_root: Path | None,
201
+ project_root: Path | None,
202
+ ) -> str:
203
+ """Return the rendered Apothem template text for a ``write_text`` entry.
204
+
205
+ Reads the manifest source and substitutes ``${HARNESS_ROOT}`` /
206
+ ``${PROJECT_ROOT}`` tokens exactly as the install pass did, so the
207
+ surgical uninstall can recognize Apothem's on-disk contribution
208
+ byte-for-byte. Returns ``""`` when the source is absent (nothing for the
209
+ structured stripper to match — operator content is then preserved).
210
+ """
211
+ src = resolve_source(entry.source)
212
+ if not src.is_file():
213
+ return ""
214
+ try:
215
+ raw = src.read_text(encoding="utf-8")
216
+ except OSError: # pragma: no cover - defensive
217
+ return ""
218
+ return render_content_tokens(
219
+ raw, harness_root=harness_root, project_root=project_root
220
+ )
221
+
222
+
223
+ def _shared_home_root_for(root: Path) -> Path:
224
+ """Return the shared working-directory root anchored at *root*.
225
+
226
+ Uninstall carries no profile, so the workspace scope defaults to
227
+ project-local and the directory name to ``.apothem`` — the base is *root*
228
+ and the shared root is ``<root>/.apothem``. This mirrors the resolution the
229
+ install pass uses on the no-profile path, so an install and its later
230
+ uninstall agree on the home's location.
231
+ """
232
+ return resolve_shared_data_home(base=root).root
233
+
234
+
235
+ def _other_harness_shares_home(*, current_harness: str, shared_root: Path) -> bool:
236
+ """Report whether another installed harness still shares *shared_root*.
237
+
238
+ The shared data home is collapsed across harnesses, so removing it on the
239
+ first uninstall would destroy data the remaining harnesses depend on. This
240
+ consults the install ledger across every package key (except
241
+ *current_harness*) and returns ``True`` when any other harness's latest
242
+ record at its install root resolves to the SAME ``shared_root`` AND that
243
+ latest record is an ``install`` (not yet uninstalled or rolled back).
244
+
245
+ A harness is "still installed at its root" when its most recent ledger
246
+ record of any kind for that root is an ``install``. Because the current
247
+ uninstall's own ``uninstall`` marker is appended only AFTER this guard runs
248
+ (see :func:`run_uninstall`), *current_harness* is excluded explicitly so it
249
+ never counts itself as a co-occupant.
250
+
251
+ The check is fail-safe: any error reading the ledger raises out to the
252
+ caller, which treats it as "cannot prove last-harness" and retains the
253
+ shared home rather than risk a destructive removal on an uncertain count.
254
+ """
255
+ for package_key in SUPPORTED_HARNESS_IDS:
256
+ if package_key == current_harness:
257
+ continue
258
+ # Find this harness's MOST RECENT record whose install root resolves to
259
+ # the same shared home. Records are append-ordered, so the last match in
260
+ # iteration order is the latest. Its kind tells the live state: an
261
+ # `install` means still installed; an `uninstall`/`rollback` means gone.
262
+ latest_kind: str | None = None
263
+ for record in install_ledger.read_records(package_key):
264
+ if _shared_home_root_for(Path(record.root)) == shared_root:
265
+ latest_kind = record.kind
266
+ if latest_kind == "install":
267
+ return True
268
+ return False
269
+
270
+
271
+ def _remove_data_home(
272
+ harness_name: str, *, root: Path, allowed_root: Path
273
+ ) -> MaterializationResult | None:
274
+ """Back up and remove the shared data home only when it is last-referenced.
275
+
276
+ The data home is the Apothem-owned ``<root>/.apothem/`` subtree shared
277
+ across every harness rooted at *root*, holding the operator's memory
278
+ records, context fragments, and learning signals (see
279
+ :func:`apothem.lib.data_home.resolve_shared_data_home`). Because it is
280
+ SHARED, removing it on the first harness uninstall would destroy data the
281
+ other still-installed harnesses depend on. The removal is therefore
282
+ conditional:
283
+
284
+ * If another installed harness still shares this home, the home is RETAINED
285
+ and an informational ``unchanged`` result is returned.
286
+ * If this is the last harness referencing the home, only the data stores
287
+ (``memory/``, ``contexts/``, ``learning/``) are backed up and removed.
288
+ ``plans/`` is NEVER auto-removed — it is operator planning state, not
289
+ Apothem-materialized config — and the ``.apothem`` root itself is left
290
+ in place so any operator ``plans/`` survives. Each removed child is copied
291
+ into the Apothem backup root first, so the data stays recoverable.
292
+
293
+ Returns ``None`` when no data store exists (nothing to remove) or the home
294
+ path falls outside the allowed write root.
295
+ """
296
+ home = _shared_home_root_for(root)
297
+ if not home.exists():
298
+ return None
299
+ if (
300
+ _validate_target_path(
301
+ home, allowed_root=allowed_root, operation="remove_data_home"
302
+ )
303
+ is not None
304
+ ):
305
+ return None
306
+
307
+ # Last-harness guard: retain the shared home while another harness still
308
+ # references it. An uncertain ledger read raises and is caught here, falling
309
+ # back to RETAIN — the safe default that never risks shared-data loss.
310
+ try:
311
+ retain = _other_harness_shares_home(
312
+ current_harness=harness_name, shared_root=home
313
+ )
314
+ except Exception: # pragma: no cover - defensive: ledger read is robust
315
+ retain = True
316
+ if retain:
317
+ return _result(
318
+ "unchanged",
319
+ "remove_data_home",
320
+ home,
321
+ "shared data home retained — another harness is still installed",
322
+ )
323
+
324
+ spec = resolve_shared_data_home(base=root)
325
+ backups: list[Path] = []
326
+ removed_any = False
327
+ # plans/ is intentionally excluded — operator planning state is never
328
+ # auto-removed by uninstall.
329
+ for child in (spec.memory, spec.contexts, spec.learning):
330
+ if not child.exists():
331
+ continue
332
+ backup = backup_existing(
333
+ child,
334
+ install_root=root,
335
+ harness_name=harness_name,
336
+ allowed_root=allowed_root,
337
+ )
338
+ if backup is not None:
339
+ backups.append(backup)
340
+ shutil.rmtree(child, onerror=_handle_rm_error)
341
+ removed_any = True
342
+ if not removed_any:
343
+ return None
344
+ return _result(
345
+ "updated",
346
+ "remove_data_home",
347
+ home,
348
+ "removed shared data stores (memory, contexts, learning); plans retained",
349
+ backup_path=backups[0] if backups else None,
350
+ )
351
+
352
+
353
+ def run_uninstall(
354
+ harness_name: str,
355
+ *,
356
+ harness_root: Path | None = None,
357
+ project_root: Path | None = None,
358
+ ) -> None:
359
+ """Remove Apothem-generated targets declared for *harness_name*.
360
+
361
+ ``write_text`` / ``sentinel_merge`` operator-owned targets are cleaned
362
+ surgically: only Apothem's contribution is stripped (the sentinel-delimited
363
+ managed block for Markdown anchors; Apothem's keys / hook handlers for JSON
364
+ and YAML configs), operator prose and operator-authored keys survive, and a
365
+ file reduced to Apothem-only content is deleted rather than left as a stub.
366
+ The pre-mutation file is copied into the Apothem backup root first — no
367
+ whole-file ``.bak`` sibling is left in the operator's directory. Directory
368
+ discovery surfaces are cleaned child-by-child so unrelated operator-authored
369
+ commands, skills, agents, and rules remain in place; existing generated
370
+ entries are backed up before removal.
371
+
372
+ The pass is ledger-driven: the latest install record for this harness+root
373
+ is the source of truth for which single-file targets were actually written,
374
+ so manifest drift after install cannot strand or over-remove them (a target
375
+ added to the manifest later is untouched; a recorded target removed from the
376
+ manifest is still cleaned). Tree/discovery surfaces stay manifest+source
377
+ driven. The per-harness data home (memory / contexts / learning) is backed up
378
+ and removed, and an uninstall marker is appended to the ledger. With no ledger
379
+ record (a pre-ledger install), the pass falls back to the full manifest.
380
+ """
381
+ rules = install_driver.load_rules(harness_name)
382
+ root = _root_for(harness_root, project_root)
383
+ allowed_root = _allowed_write_root(harness_root, project_root)
384
+
385
+ # Ledger-driven: the latest install record is the source of truth for what
386
+ # this harness+root actually wrote. ``recorded_paths`` is None when no record
387
+ # exists (legacy / pre-ledger install) — fall back to removing every manifest
388
+ # target. With a record, a single-file manifest target is removed only if it
389
+ # was recorded, so an entry added to the manifest after install is not touched.
390
+ record = install_ledger.latest_record(harness_name, root=root)
391
+ recorded_paths: set[str] | None = (
392
+ {target.path for target in record.targets} if record is not None else None
393
+ )
394
+ handled: set[str] = set()
395
+
396
+ for entry in rules.install:
397
+ if entry.mode in {"write_text", "sentinel_merge"}:
398
+ target = resolve_target(
399
+ entry.target,
400
+ harness_root=harness_root,
401
+ project_root=project_root,
402
+ )
403
+ if recorded_paths is not None and _path_text(target) not in recorded_paths:
404
+ continue
405
+ template_text = _rendered_template_text(
406
+ entry, harness_root=harness_root, project_root=project_root
407
+ )
408
+ _surgical_remove_from_target(
409
+ target,
410
+ template_text,
411
+ mode=entry.mode,
412
+ install_root=root,
413
+ harness_name=harness_name,
414
+ allowed_root=allowed_root,
415
+ )
416
+ handled.add(_path_text(target))
417
+ continue
418
+ # Tree/discovery surfaces are reversed child-by-child against the apothem
419
+ # source enumeration so operator-authored siblings survive — a path list
420
+ # cannot express that, so these stay manifest+source-driven.
421
+ for target in _generated_targets_for_entry(
422
+ entry,
423
+ harness_root=harness_root,
424
+ project_root=project_root,
425
+ exclude=rules.exclude,
426
+ ):
427
+ _replace_path(
428
+ target,
429
+ install_root=root,
430
+ harness_name=harness_name,
431
+ allowed_root=allowed_root,
432
+ )
433
+ handled.add(_path_text(target))
434
+
435
+ # Recorded sentinel anchors not covered by a current manifest entry: the
436
+ # bolt-on profile anchors (claude-code ``CLAUDE.md``, the single-file adapters'
437
+ # profile rule) and any sentinel entry removed from the manifest after install.
438
+ # The managed block self-delimits, so it strips without the template.
439
+ if record is not None:
440
+ for recorded in record.targets:
441
+ if recorded.path in handled or recorded.mode != "sentinel_merge":
442
+ continue
443
+ _surgical_remove_from_target(
444
+ Path(recorded.path),
445
+ "",
446
+ mode="sentinel_merge",
447
+ install_root=root,
448
+ harness_name=harness_name,
449
+ allowed_root=allowed_root,
450
+ )
451
+ handled.add(recorded.path)
452
+
453
+ # Back up and remove the per-harness data home (memory / contexts / learning).
454
+ _remove_data_home(harness_name, root=root, allowed_root=allowed_root)
455
+
456
+ # Append an uninstall marker referencing the install pass it reversed.
457
+ install_ledger.append_record(
458
+ LedgerRecord.create(
459
+ harness=harness_name,
460
+ root=root,
461
+ kind="uninstall",
462
+ install_id=record.install_id if record is not None else None,
463
+ )
464
+ )
465
+
466
+
467
+ def build_plan(
468
+ harness_name: str,
469
+ *,
470
+ harness_root: Path | None = None,
471
+ project_root: Path | None = None,
472
+ ) -> list[dict[str, str]]:
473
+ """Return *harness_name*'s propagation plan without writing anything.
474
+
475
+ Each entry carries ``source`` (resolved on-disk path), ``target``
476
+ (resolved against the supplied root), and ``mode``. When the relevant
477
+ root is ``None`` the corresponding placeholder stays literal in the
478
+ target string so the operator sees the unresolved template form instead
479
+ of a misleading absolute path.
480
+ """
481
+ rules = install_driver.load_rules(harness_name)
482
+ return [
483
+ {
484
+ "source": str(resolve_source(entry.source)),
485
+ "target": str(
486
+ resolve_target(
487
+ entry.target,
488
+ harness_root=harness_root,
489
+ project_root=project_root,
490
+ )
491
+ ),
492
+ "mode": entry.mode,
493
+ }
494
+ for entry in rules.install
495
+ ]