wikifier 4.6.1__tar.gz → 4.6.3__tar.gz

{wikifier-4.6.1/wikifier.egg-info → wikifier-4.6.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: wikifier
-Version: 4.6.1
+Version: 4.6.3
 Summary: Zero-dependency agent-to-agent codebase wiki for LLMs and AI agents. Autonomously maintained via record-change and mark-green for token-efficient lookup of files, dependencies, health, and summaries — across tiny scripts to 50k+ monorepos. Optional MCP server with rich tools for agents.
 Author-email: Aron Amos <aron@example.com>
 Maintainer: Aron Amos
@@ -84,27 +84,33 @@ Always set an explicit root for external trees: `WIKIFIER_PROJECT_ROOT=/abs/path
 
 ## Steady state (only touch what needs it)
 
-Full protocol: [`skills/run.md`](skills/run.md).
+Full protocol: [`skills/run.md`](skills/run.md) (Agent Protocol v0.6 — package **4.6.x**).
 
 ```bash
-wikifier check-changes          # yellow dirty files; red ghosts (missing paths)
-# prioritize 🔴 then 🟡 — do NOT re-wiki 🟢 Green files
+wikifier session-bootstrap      # one-shot: root, health, attention, actions[]
+wikifier check-changes          # content-honest dirty; red ghosts (missing paths)
+# prioritize 🔴 then *actionable* 🟡 — do NOT re-wiki 🟢 Green files
+wikifier prepare-edit path/file.py   # wiki + status + deps/dependents preflight
 # ... edit only those sources ...
 wikifier record-change "path/file.py" "why this changed"   # required
 # ... refresh that file’s wiki summary only ...
 wikifier mark-green "path/file.py"
-wikifier update-maps            # only if imports/structure changed
+wikifier update-maps            # only if imports/structure changed (warm 0-dirty is cheap)
 # removals:
 wikifier record-deletion "path/gone.py" "why removed"
 ```
 
-MCP **Core 6** (start every session): `get_project_status`, `check_changes`, `get_files_needing_attention`, `get_file_wiki`, `suggest_next_actions`, `record_change` / `mark_green`. Intel as needed: `get_dependencies`, `get_dependents`, `get_cycles`. Always pass `project_root=` for external trees.
+**Core 6** (prefer every session — MCP or library/CLI):  
+`session_bootstrap` → `check_changes` → `prepare_edit` → `suggest_next_actions` (json `actions[]`) → `record_change` → `mark_green`.
+
+Advanced intel as needed: `get_dependencies`, `get_dependents`, `get_cycles`, barrels/diagnostics. Always pass `project_root=` / `WIKIFIER_PROJECT_ROOT` for external trees. **Never** point `project_root` at a multi-repo parent folder (e.g. a directory of clones).
 
 ## What you get
 
-- **Import analysis** — Python, JS/TS (ESM/CJS, barrels), Rust, Go, C/C++ includes, C# usings; per-edge confidence; name-routed barrel expansion for TS/JS
+- **Import analysis** — Python, JS/TS (ESM/CJS, barrels), Rust (`use`/`mod` + best-effort `crate::` paths), Go, C/C++ includes, C# usings; per-edge confidence; barrel expansion for TS/JS
 - **Incremental pipeline** — pure-Python `update-maps`: dirty parse → import cache → reverse deps → cycles → `library.md`
-- **Selective agent work** — health + suggest bias to 🔴/🟡 only; ACS *actionable* low-conf excludes stdlib/external noise
+- **Warm agent maps (4.6.3+)** — zero-dirty fast path skips full graph/`library.md` rewrite when nothing reparsed; content-hash dirty so mtime thrash ≠ reparse; `--directory=` scopes the candidate walk (monorepo budgets)
+- **Selective agent work** — health + suggest bias to 🔴/actionable 🟡 only; **ACS v1.3** `reason_code` / `agent_signal` (`skip`|`investigate`); prefer `actionable_low_conf_edges` over raw low-conf noise
 - **Scale** — reverse index + barrel invalidation so one edit doesn’t re-scan the monorepo
 - **MCP tools** — optional server for Claude, Cursor, Cline, and other MCP clients
 - **Zero core dependencies** — stdlib only; forks can add their own stack on top
@@ -112,32 +118,45 @@ MCP **Core 6** (start every session): `get_project_status`, `check_changes`, `ge
 
 ## Performance (measured)
 
-| Project | Scale | Full `update-maps` |
-|---------|-------|--------------------|
-| llama_index | ~3.8k Python files | ~8.5s |
-| Babylon.js | ~3.9k TS files, barrel-heavy | ~4.5 min (scoped re-runs ~80s) |
-| Large trees (e.g. LLVM-scale) | tens of thousands of files | candidate scan in seconds |
+Full / heavy runs (historical order-of-magnitude):
+
+| Project | Scale | Full / heavy `update-maps` |
+|---------|-------|----------------------------|
+| llama_index | ~3.8k Python files | ~8.5s class full |
+| Babylon.js | ~3.9k TS files, barrel-heavy | minutes full; scoped re-runs tens of seconds |
+| Large trees (e.g. LLVM-scale) | tens of thousands of files | use lean monitor + `--directory` / `--max-files` |
+
+Warm **0-dirty** re-runs after 4.6.3 (same machine; scoped where noted) — agent session path:
+
+| Project | Scope | Warm2 `update-maps` |
+|---------|-------|---------------------|
+| Wikifier (self) | incremental full | ~43 ms |
+| redox | `src` | ~17 ms |
+| llama_index | `llama-index-core` | ~0.6 s |
+| rust | `library/std/src` (budgeted) | ~0.7 s (vs multi-second full-tree walk before scoped collect) |
 
-Tests: `python -m unittest discover tests` (stdlib only).
+Tests: `python -m unittest discover tests` (stdlib only; 86+ cases including agent-scale edges).
 
 ## Commands
 
 | Command | Purpose |
 |---------|---------|
 | `wikifier init [--target DIR]` | Bootstrap project + human `index.html` |
-| `wikifier check-changes` | Incremental scan → health / pending |
+| `wikifier session-bootstrap` | Session start: health, attention, dispatchable `actions[]` |
+| `wikifier check-changes` | Content-honest scan → health / pending |
+| `wikifier prepare-edit <file>` | Preflight: status, wiki snippet, deps, dependents |
 | `wikifier record-change <file> "reason"` | Log *why* (required after edits) |
-| `wikifier mark-green <file>` | Mark wiki current |
+| `wikifier mark-green <file>` | Mark wiki current + source content-hash baseline |
 | `wikifier record-deletion <file> "reason"` | Mark removed paths 🔴 + prune barrel refs |
-| `wikifier suggest-next` | Next actions (🔴/🟡 only) |
-| `wikifier update-maps [--directory=src/] [--max-files=N]` | Rebuild graph + `library.md` |
+| `wikifier suggest-next` | Next actions (🔴/actionable 🟡 only; `--json` for `actions[]`) |
+| `wikifier update-maps [--directory=src/] [--max-files=N]` | Rebuild graph + `library.md` (warm 0-dirty is fast) |
 | `wikifier health [--summary\|--json]` | Health matrix (machine-friendly flags) |
 | `wikifier validate` | Missing wiki rows + ghost paths |
 | `wikifier cycles` | Circular deps + break hints |
 | `wikifier monitor` / `daemon` | Background maintenance (`WIKIFIER_DAEMON_MAPS=0` for check-only) |
 | `wikifier serve` | Localhost dashboard with Run/Stop |
 
-Library: `from wikifier import check_changes, record_change, mark_green, suggest_next_actions, update_maps, health`.
+Library: `from wikifier import session_bootstrap, prepare_edit, check_changes, record_change, mark_green, suggest_next_actions, update_maps, health, list_core_tools`.
 
 ## MCP
 

{wikifier-4.6.1 → wikifier-4.6.3}/README.md

@@ -52,27 +52,33 @@ Always set an explicit root for external trees: `WIKIFIER_PROJECT_ROOT=/abs/path
 
 ## Steady state (only touch what needs it)
 
-Full protocol: [`skills/run.md`](skills/run.md).
+Full protocol: [`skills/run.md`](skills/run.md) (Agent Protocol v0.6 — package **4.6.x**).
 
 ```bash
-wikifier check-changes          # yellow dirty files; red ghosts (missing paths)
-# prioritize 🔴 then 🟡 — do NOT re-wiki 🟢 Green files
+wikifier session-bootstrap      # one-shot: root, health, attention, actions[]
+wikifier check-changes          # content-honest dirty; red ghosts (missing paths)
+# prioritize 🔴 then *actionable* 🟡 — do NOT re-wiki 🟢 Green files
+wikifier prepare-edit path/file.py   # wiki + status + deps/dependents preflight
 # ... edit only those sources ...
 wikifier record-change "path/file.py" "why this changed"   # required
 # ... refresh that file’s wiki summary only ...
 wikifier mark-green "path/file.py"
-wikifier update-maps            # only if imports/structure changed
+wikifier update-maps            # only if imports/structure changed (warm 0-dirty is cheap)
 # removals:
 wikifier record-deletion "path/gone.py" "why removed"
 ```
 
-MCP **Core 6** (start every session): `get_project_status`, `check_changes`, `get_files_needing_attention`, `get_file_wiki`, `suggest_next_actions`, `record_change` / `mark_green`. Intel as needed: `get_dependencies`, `get_dependents`, `get_cycles`. Always pass `project_root=` for external trees.
+**Core 6** (prefer every session — MCP or library/CLI):  
+`session_bootstrap` → `check_changes` → `prepare_edit` → `suggest_next_actions` (json `actions[]`) → `record_change` → `mark_green`.
+
+Advanced intel as needed: `get_dependencies`, `get_dependents`, `get_cycles`, barrels/diagnostics. Always pass `project_root=` / `WIKIFIER_PROJECT_ROOT` for external trees. **Never** point `project_root` at a multi-repo parent folder (e.g. a directory of clones).
 
 ## What you get
 
-- **Import analysis** — Python, JS/TS (ESM/CJS, barrels), Rust, Go, C/C++ includes, C# usings; per-edge confidence; name-routed barrel expansion for TS/JS
+- **Import analysis** — Python, JS/TS (ESM/CJS, barrels), Rust (`use`/`mod` + best-effort `crate::` paths), Go, C/C++ includes, C# usings; per-edge confidence; barrel expansion for TS/JS
 - **Incremental pipeline** — pure-Python `update-maps`: dirty parse → import cache → reverse deps → cycles → `library.md`
-- **Selective agent work** — health + suggest bias to 🔴/🟡 only; ACS *actionable* low-conf excludes stdlib/external noise
+- **Warm agent maps (4.6.3+)** — zero-dirty fast path skips full graph/`library.md` rewrite when nothing reparsed; content-hash dirty so mtime thrash ≠ reparse; `--directory=` scopes the candidate walk (monorepo budgets)
+- **Selective agent work** — health + suggest bias to 🔴/actionable 🟡 only; **ACS v1.3** `reason_code` / `agent_signal` (`skip`|`investigate`); prefer `actionable_low_conf_edges` over raw low-conf noise
 - **Scale** — reverse index + barrel invalidation so one edit doesn’t re-scan the monorepo
 - **MCP tools** — optional server for Claude, Cursor, Cline, and other MCP clients
 - **Zero core dependencies** — stdlib only; forks can add their own stack on top
@@ -80,32 +86,45 @@ MCP **Core 6** (start every session): `get_project_status`, `check_changes`, `ge
 
 ## Performance (measured)
 
-| Project | Scale | Full `update-maps` |
-|---------|-------|--------------------|
-| llama_index | ~3.8k Python files | ~8.5s |
-| Babylon.js | ~3.9k TS files, barrel-heavy | ~4.5 min (scoped re-runs ~80s) |
-| Large trees (e.g. LLVM-scale) | tens of thousands of files | candidate scan in seconds |
+Full / heavy runs (historical order-of-magnitude):
+
+| Project | Scale | Full / heavy `update-maps` |
+|---------|-------|----------------------------|
+| llama_index | ~3.8k Python files | ~8.5s class full |
+| Babylon.js | ~3.9k TS files, barrel-heavy | minutes full; scoped re-runs tens of seconds |
+| Large trees (e.g. LLVM-scale) | tens of thousands of files | use lean monitor + `--directory` / `--max-files` |
+
+Warm **0-dirty** re-runs after 4.6.3 (same machine; scoped where noted) — agent session path:
+
+| Project | Scope | Warm2 `update-maps` |
+|---------|-------|---------------------|
+| Wikifier (self) | incremental full | ~43 ms |
+| redox | `src` | ~17 ms |
+| llama_index | `llama-index-core` | ~0.6 s |
+| rust | `library/std/src` (budgeted) | ~0.7 s (vs multi-second full-tree walk before scoped collect) |
 
-Tests: `python -m unittest discover tests` (stdlib only).
+Tests: `python -m unittest discover tests` (stdlib only; 86+ cases including agent-scale edges).
 
 ## Commands
 
 | Command | Purpose |
 |---------|---------|
 | `wikifier init [--target DIR]` | Bootstrap project + human `index.html` |
-| `wikifier check-changes` | Incremental scan → health / pending |
+| `wikifier session-bootstrap` | Session start: health, attention, dispatchable `actions[]` |
+| `wikifier check-changes` | Content-honest scan → health / pending |
+| `wikifier prepare-edit <file>` | Preflight: status, wiki snippet, deps, dependents |
 | `wikifier record-change <file> "reason"` | Log *why* (required after edits) |
-| `wikifier mark-green <file>` | Mark wiki current |
+| `wikifier mark-green <file>` | Mark wiki current + source content-hash baseline |
 | `wikifier record-deletion <file> "reason"` | Mark removed paths 🔴 + prune barrel refs |
-| `wikifier suggest-next` | Next actions (🔴/🟡 only) |
-| `wikifier update-maps [--directory=src/] [--max-files=N]` | Rebuild graph + `library.md` |
+| `wikifier suggest-next` | Next actions (🔴/actionable 🟡 only; `--json` for `actions[]`) |
+| `wikifier update-maps [--directory=src/] [--max-files=N]` | Rebuild graph + `library.md` (warm 0-dirty is fast) |
 | `wikifier health [--summary\|--json]` | Health matrix (machine-friendly flags) |
 | `wikifier validate` | Missing wiki rows + ghost paths |
 | `wikifier cycles` | Circular deps + break hints |
 | `wikifier monitor` / `daemon` | Background maintenance (`WIKIFIER_DAEMON_MAPS=0` for check-only) |
 | `wikifier serve` | Localhost dashboard with Run/Stop |
 
-Library: `from wikifier import check_changes, record_change, mark_green, suggest_next_actions, update_maps, health`.
+Library: `from wikifier import session_bootstrap, prepare_edit, check_changes, record_change, mark_green, suggest_next_actions, update_maps, health, list_core_tools`.
 
 ## MCP
 

{wikifier-4.6.1 → wikifier-4.6.3}/skills/run.md

@@ -43,8 +43,10 @@ Do **not** open megamodules (`javascript.py`, `import_cache.py`, `bree.py`) to d
 |------|-----|
 | First-run map | `init` → `update-maps` → `health --summary` → `suggest-next` |
 | **Session start (4.6+)** | `session_bootstrap` (or CLI `session-bootstrap`) — one shot: root, health, attention, `actions[]` |
+| **Core tool list** | `list_core_tools` / bootstrap `core_surface` — prefer Core 6; advanced is non-core |
 | Steady-state | `check-changes` (content-honest) → edit 🔴/actionable 🟡 only → `record-change` → wiki → `mark-green` |
-| **Preflight edit** | `prepare_edit` / CLI `prepare-edit <file>` — wiki + status + deps + dependents |
+| **Hash migration** | `seed_source_content_hashes` / CLI `seed-source-hashes` — baseline Greens without mass Yellow |
+| **Preflight edit** | `prepare_edit` / CLI `prepare-edit <file>` — wiki + status + deps + dependents (multi-shape reverse index) |
 | **Why / journal** | `why_file` / `search_journal` — semantic trail, not mtime theater |
 | Lookup Core | `session_bootstrap`, `check_changes`, `prepare_edit`, `suggest_next_actions` (json `actions[]`), `record_change`, `mark_green` |
 | Advanced intel | `get_dependencies`, `get_dependents`, `get_cycles`, barrel/diagnostics — not daily Core |

{wikifier-4.6.1 → wikifier-4.6.3}/tests/test_agent_loop.py

@@ -222,5 +222,107 @@ class TestCliBootstrapEntry(TempProjectTestCase):
         self.assertIn("actions", res)
 
 
+class TestSeedSourceHashes(TempProjectTestCase):
+    def test_seed_then_touch_ok_rewrite_yellows(self):
+        p = self.write("seeded.py", "print(0)\n")
+        health_mod.upsert_entry(self.root, "seeded.py", "🟢 Green", "legacy no hash")
+        data = health_mod.load_health(self.root)
+        self.assertNotIn("source_content_hash", data["entries"]["seeded.py"] or {})
+        res = health_mod.seed_source_content_hashes(self.root, only_green=True)
+        self.assertTrue(res.get("success"), res)
+        self.assertGreaterEqual(int(res.get("seeded") or 0), 1)
+        data2 = health_mod.load_health(self.root)
+        ent = data2["entries"]["seeded.py"]
+        self.assertIn("Green", ent["status"])
+        self.assertTrue(ent.get("source_content_hash"))
+        baseline = ent["source_content_hash"]
+        from wikifier import import_cache as ic
+        cache = {}
+        ic.update_file_data(cache, "seeded.py", mtime=1, imports=[], resolved_pairs=[])
+        ic.save_cache(self.root, cache)
+        os.utime(p, None)
+        cache = ic.load_cache(self.root)
+        cache["seeded.py"]["mtime"] = 1
+        ic.save_cache(self.root, cache)
+        r = cli.check_changes(project_root=self.root)
+        self.assertTrue(r.get("success"), r)
+        data3 = health_mod.load_health(self.root)
+        self.assertIn("Green", data3["entries"]["seeded.py"]["status"])
+        self.assertEqual(data3["entries"]["seeded.py"]["source_content_hash"], baseline)
+        p.write_text("print(99)\n", encoding="utf-8")
+        cache = ic.load_cache(self.root)
+        cache["seeded.py"]["mtime"] = 1
+        ic.save_cache(self.root, cache)
+        r2 = cli.check_changes(project_root=self.root)
+        self.assertTrue(r2.get("success"), r2)
+        self.assertGreaterEqual(int(r2.get("changes_detected") or 0), 1)
+        data4 = health_mod.load_health(self.root)
+        self.assertIn("Yellow", data4["entries"]["seeded.py"]["status"])
+
+
+class TestCoreSurfaceListing(unittest.TestCase):
+    def test_list_core_tools_has_six(self):
+        from wikifier.agent_loop import list_core_tools, CORE_DAILY_NAMES
+        res = list_core_tools()
+        self.assertTrue(res.get("success"))
+        self.assertEqual(res.get("core_count"), 6)
+        names = res.get("core_names") or []
+        for n in (
+            "session_bootstrap", "check_changes", "prepare_edit",
+            "suggest_next_actions", "record_change", "mark_green",
+        ):
+            self.assertIn(n, names)
+        self.assertEqual(names, CORE_DAILY_NAMES)
+        adv = res.get("advanced_intel") or []
+        self.assertTrue(adv)
+        self.assertNotIn("session_bootstrap", adv)  # core not listed as advanced-only
+
+
+class TestPrepareEditReverseShapes(TempProjectTestCase):
+    def test_flat_and_nested_reverse_index(self):
+        self.write("lib/t.py", "x=1\n")
+        health_mod.upsert_entry(self.root, "lib/t.py", "🟢 Green", "ok")
+        from wikifier import import_cache as ic
+        from wikifier.agent_loop import prepare_edit, resolve_dependents_from_cache
+
+        # Flat shape
+        cache_flat = {
+            "lib/t.py": {"mtime": 1, "resolved_pairs": []},
+            "lib/a.py": {"mtime": 1, "resolved_pairs": [{"resolved": "lib/t.py", "resolved_path": "lib/t.py"}]},
+            "_reverse_dependencies": {"lib/t.py": ["lib/a.py", "lib/b.py"]},
+        }
+        deps = resolve_dependents_from_cache(cache_flat, "lib/t.py")
+        self.assertIn("lib/a.py", deps)
+        self.assertIn("lib/b.py", deps)
+        ic.save_cache(self.root, cache_flat)
+        pe = prepare_edit("lib/t.py", project_root=self.root)
+        self.assertTrue(pe.get("success"))
+        self.assertIn("lib/a.py", pe.get("dependents") or [])
+
+        # Nested index shape
+        cache_nest = {
+            "lib/t.py": {"mtime": 1, "resolved_pairs": []},
+            "_reverse_dependencies": {
+                "index": {"lib/t.py": ["lib/nested1.py", "lib/nested2.py"]},
+                "version": 1,
+            },
+        }
+        deps2 = resolve_dependents_from_cache(cache_nest, "lib/t.py")
+        self.assertEqual(set(deps2), {"lib/nested1.py", "lib/nested2.py"})
+        ic.save_cache(self.root, cache_nest)
+        pe2 = prepare_edit("lib/t.py", project_root=self.root)
+        self.assertTrue(pe2.get("success"))
+        self.assertIn("lib/nested1.py", pe2.get("dependents") or [])
+
+        # Dict value shape
+        cache_dict = {
+            "_reverse_dependencies": {
+                "lib/t.py": {"importers": ["lib/from_dict.py"]},
+            }
+        }
+        deps3 = resolve_dependents_from_cache(cache_dict, "lib/t.py")
+        self.assertIn("lib/from_dict.py", deps3)
+
+
 if __name__ == "__main__":
     unittest.main()

wikifier-4.6.3/tests/test_agent_scale.py

@@ -0,0 +1,244 @@
+"""Agent-scale perf/accuracy path tests (zero-dirty, content-hash dirty, ACS v1.3).
+
+Drives shipped library APIs only — no reimplementation of the unit under test.
+"""
+
+from __future__ import annotations
+
+import os
+import time
+import unittest
+from pathlib import Path
+
+from tests._base import TempProjectTestCase
+
+from wikifier import cli
+from wikifier import import_cache as ic
+from wikifier.import_cache import (
+    classify_edge_agent_signal,
+    compute_acs_summary,
+    compute_file_content_hash,
+)
+
+
+class TestContentHashDirty(TempProjectTestCase):
+    def test_mtime_thrash_does_not_reparse_when_content_hash_matches(self):
+        p = self.write("pkg/a.py", "import os\nx = 1\n")
+        # First map: populates cache + content_hash
+        r1 = cli.update_maps(project_root=self.root, full=True)
+        self.assertTrue(r1.get("success"), r1)
+        self.assertGreaterEqual(int(r1.get("files_parsed") or 0), 1)
+        cache = ic.load_cache(self.root)
+        ent = cache.get("pkg/a.py") or cache.get("a.py")
+        # find entry
+        if ent is None:
+            for k, v in cache.items():
+                if str(k).endswith("a.py") and isinstance(v, dict):
+                    ent = v
+                    break
+        self.assertIsInstance(ent, dict, msg=f"cache keys={list(cache)[:20]}")
+        self.assertIn("content_hash", ent)
+        stored = ent["content_hash"]
+        live = compute_file_content_hash(p)
+        self.assertEqual(stored, live)
+
+        # Force stale mtime in cache, then touch file (same bytes)
+        ent["mtime"] = 1
+        ic.save_cache(self.root, cache)
+        time.sleep(0.05)
+        os.utime(p, None)
+
+        updates = []
+        need = ic.compute_files_needing_reparse(
+            self.root, [p], full_rebuild=False, content_stable_mtime_updates=updates
+        )
+        self.assertEqual(need, [], msg=f"should not reparse content-stable; updates={updates}")
+        self.assertGreaterEqual(len(updates), 1)
+
+    def test_content_change_does_reparse(self):
+        p = self.write("b.py", "y = 1\n")
+        r1 = cli.update_maps(project_root=self.root, full=True)
+        self.assertTrue(r1.get("success"), r1)
+        cache = ic.load_cache(self.root)
+        ent = cache.get("b.py")
+        self.assertIsInstance(ent, dict)
+        ent["mtime"] = 1
+        # Keep old hash so mtime+hash mismatch forces reparse after rewrite
+        ic.save_cache(self.root, cache)
+        p.write_text("y = 2\n", encoding="utf-8")
+        time.sleep(0.02)
+        need = ic.compute_files_needing_reparse(self.root, [p], full_rebuild=False)
+        self.assertEqual(len(need), 1)
+        self.assertEqual(need[0].resolve(), p.resolve())
+
+
+class TestZeroDirtyFastPath(TempProjectTestCase):
+    def test_second_update_maps_uses_fast_path(self):
+        self.write("m.py", "print(1)\n")
+        r1 = cli.update_maps(project_root=self.root, full=True)
+        self.assertTrue(r1.get("success"), r1)
+        # Ensure library exists so fast path can skip rewrite
+        self.assertTrue((self.root / "library.md").is_file() or r1.get("library", {}).get("success"))
+
+        r2 = cli.update_maps(project_root=self.root, full=False)
+        self.assertTrue(r2.get("success"), r2)
+        self.assertEqual(int(r2.get("files_parsed") or 0), 0)
+        self.assertEqual(int(r2.get("files_to_reparse") or 0), 0)
+        self.assertTrue(r2.get("zero_dirty_fast_path"), r2)
+        lib = r2.get("library") or {}
+        self.assertTrue(lib.get("success"), lib)
+        # Prefer skip when library already present
+        if (self.root / "library.md").is_file():
+            self.assertTrue(lib.get("skipped") or lib.get("path"))
+
+    def test_zero_dirty_persists_acs_v13_to_disk(self):
+        """Warm zero-dirty path must write ACS 1.3 + reason_code_counts to import_cache."""
+        self.write("n.py", "import os\nx=1\n")
+        r1 = cli.update_maps(project_root=self.root, full=True)
+        self.assertTrue(r1.get("success"), r1)
+        # Simulate pre-1.3 cache left on disk (the bug: warm path upgraded memory only)
+        cache = ic.load_cache(self.root)
+        cache["_acs_summary"] = {
+            "acs_version": "1.2",
+            "total_scored_edges": 1,
+            "avg_confidence": 0.5,
+            "low_conf_edges": 1,
+            "actionable_low_conf_edges": 0,
+        }
+        ic.save_cache(self.root, cache)
+        on_disk = ic.load_cache(self.root)
+        self.assertEqual(str((on_disk.get("_acs_summary") or {}).get("acs_version")), "1.2")
+
+        r2 = cli.update_maps(project_root=self.root, full=False)
+        self.assertTrue(r2.get("success"), r2)
+        self.assertTrue(r2.get("zero_dirty_fast_path"), r2)
+        self.assertEqual((r2.get("acs") or {}).get("acs_version"), "1.3")
+
+        reloaded = ic.load_cache(self.root)
+        acs = reloaded.get("_acs_summary") or {}
+        self.assertEqual(acs.get("acs_version"), "1.3", msg=acs)
+        self.assertIn("reason_code_counts", acs)
+        self.assertIsInstance(acs.get("reason_code_counts"), dict)
+
+    def test_max_files_skip_honesty(self):
+        for i in range(5):
+            self.write(f"f{i}.py", f"v = {i}\n")
+        r = cli.update_maps(project_root=self.root, full=True, max_files=2)
+        self.assertTrue(r.get("success"), r)
+        self.assertEqual(int(r.get("files_parsed") or 0), 2)
+        self.assertEqual(int(r.get("files_skipped") or 0), 3)
+
+
+class TestACSv13(TempProjectTestCase):
+    def test_classify_edge_reason_codes(self):
+        ext = {
+            "raw": "os",
+            "resolved": "",
+            "confidence_score": 0.48,
+            "diagnostic": {"category": "external_or_bare"},
+            "resolution_metadata": {"strategy": "python-bare-or-external"},
+        }
+        sig = classify_edge_agent_signal(ext)
+        self.assertEqual(sig["agent_signal"], "skip")
+        self.assertEqual(sig["reason_code"], "external_or_bare")
+        self.assertFalse(sig["actionable"])
+
+        unres = {"raw": ".missing", "resolved": "", "confidence_score": 0.4}
+        sig2 = classify_edge_agent_signal(unres)
+        self.assertEqual(sig2["agent_signal"], "investigate")
+        self.assertEqual(sig2["reason_code"], "unresolved_project")
+        self.assertTrue(sig2["actionable"])
+
+        ok = {"raw": "./x", "resolved": "x.py", "confidence_score": 0.95}
+        sig3 = classify_edge_agent_signal(ok)
+        self.assertEqual(sig3["reason_code"], "high_confidence_ok")
+        self.assertFalse(sig3["actionable"])
+
+    def test_compute_acs_summary_v13_shape(self):
+        cache = {
+            "a.py": {
+                "mtime": 1,
+                "resolved_pairs": [
+                    {
+                        "raw": "os",
+                        "resolved": "",
+                        "confidence_score": 0.48,
+                        "diagnostic": {"category": "external_or_bare"},
+                        "resolution_metadata": {"strategy": "python-bare-or-external"},
+                    },
+                    {
+                        "raw": ".b",
+                        "resolved": "b.py",
+                        "confidence_score": 0.5,
+                        "confidence_explanation": "low internal",
+                    },
+                    {
+                        "raw": ".missing",
+                        "resolved": "",
+                        "confidence_score": 0.4,
+                        "confidence_explanation": "unresolved project",
+                    },
+                ],
+            }
+        }
+        acs = compute_acs_summary(cache)
+        self.assertEqual(acs["acs_version"], "1.3")
+        self.assertIn("reason_code_counts", acs)
+        self.assertIn("agent_signal_counts", acs)
+        self.assertGreaterEqual(acs["actionable_low_conf_edges"], 2)
+        self.assertGreaterEqual(acs["external_noise_edges"], 1)
+        self.assertIn("investigate", acs["agent_signal_counts"])
+
+
+class TestCoreLoopEdges(TempProjectTestCase):
+    def test_session_bootstrap_and_prepare_edit(self):
+        self.write("hub.py", "import os\n")
+        cli.update_maps(project_root=self.root, full=True)
+        boot = cli.session_bootstrap(project_root=self.root)
+        self.assertTrue(boot.get("success"), boot)
+        self.assertIn("actions", boot)
+        pe = cli.prepare_edit("hub.py", project_root=self.root)
+        self.assertTrue(pe.get("success"), pe)
+        self.assertIn("status", pe)
+
+    def test_invalid_project_root_structured(self):
+        # missing path should not crash core helpers
+        missing = self.root / "no_such_project_dir"
+        r = cli.check_changes(project_root=missing)
+        self.assertIsInstance(r, dict)
+        # either success with empty or structured failure — never exception
+        self.assertIn("success", r)
+
+    def test_prepare_edit_missing_file_fails(self):
+        r = cli.prepare_edit("does_not_exist_xyz.py", project_root=self.root)
+        self.assertIsInstance(r, dict)
+        self.assertFalse(r.get("success"), r)
+        self.assertIn("error", r)
+
+    def test_multi_repo_parent_scope_warning_or_ok_flag(self):
+        # Bootstrap on a real root must set scope.ok; parent-of-many is agent anti-pattern
+        boot = cli.session_bootstrap(project_root=self.root)
+        self.assertTrue(boot.get("success"), boot)
+        scope = boot.get("scope") or {}
+        self.assertIn("ok", scope)
+
+
+class TestRustCrateResolve(TempProjectTestCase):
+    def test_crate_use_resolves_sibling_module(self):
+        from wikifier.parsers import rust as rust_parser
+
+        lib = self.write("src/lib.rs", "mod foo;\npub use crate::foo::bar;\n")
+        self.write("src/foo.rs", "pub fn bar() {}\n")
+        edges = rust_parser.parse_rust_imports(str(lib))
+        uses = [e for e in edges if e.get("statement_type") == "use"]
+        self.assertTrue(uses)
+        # at least one use should resolve to foo.rs when crate path works
+        resolved_any = [e for e in uses if e.get("resolved_path")]
+        self.assertTrue(
+            resolved_any,
+            msg=f"expected crate:: resolve; edges={uses}",
+        )
+
+
+if __name__ == "__main__":
+    unittest.main()

{wikifier-4.6.1 → wikifier-4.6.3}/tests/test_gap_closure.py

@@ -104,7 +104,7 @@ class TestAcsActionableG4(TempProjectTestCase):
         ))
 
     def test_dynamic_literal_noise_demoted_from_actionable(self):
-        """ACS v1.2: importlib.import_module(\"pkg\") static dynamics are not actionable."""
+        """ACS v1.2+: importlib.import_module(\"pkg\") static dynamics are not actionable."""
         dyn_lit = {
             "raw": "\"wikifier.health\"",
             "resolved": "wikifier.health",
@@ -142,10 +142,13 @@ class TestAcsActionableG4(TempProjectTestCase):
         self.assertTrue(ic._edge_is_dynamic_literal_noise(dyn_lit))
         self.assertFalse(ic._edge_is_dynamic_literal_noise(project_fragile))
         summary = ic.compute_acs_summary(cache)
-        self.assertEqual(summary.get("acs_version"), "1.2")
+        # v1.3 additive (reason codes); still demotes dynamic literals from actionable
+        self.assertGreaterEqual(str(summary.get("acs_version") or ""), "1.2")
         self.assertGreaterEqual(summary["low_conf_edges"], 2)
         self.assertEqual(summary["actionable_low_conf_edges"], 1)
         self.assertGreaterEqual(summary.get("dynamic_literal_noise_edges", 0), 1)
+        if "reason_code_counts" in summary:
+            self.assertIn("dynamic_literal", summary["reason_code_counts"] or {})
         action = ic.get_low_confidence_edges(cache, actionable_only=True)
         self.assertEqual(len(action), 1)
         self.assertIn("missing_local", str(action[0].get("raw") or action[0].get("resolved")))

{wikifier-4.6.1 → wikifier-4.6.3}/wikifier/__init__.py

@@ -46,6 +46,8 @@ from .cli import (
     prepare_edit,
     search_journal,
     why_file,
+    seed_source_content_hashes,
+    list_core_tools,
 )
 from . import agent_loop
 
@@ -76,4 +78,4 @@ from .contracts import (
     compute_acs_confidence,
 )
 
-__version__ = "4.6.1"
+__version__ = "4.6.3"