wikifier 4.5.0__tar.gz → 4.5.2__tar.gz

wikifier-4.5.2/PKG-INFO

@@ -0,0 +1,154 @@
+Metadata-Version: 2.4
+Name: wikifier
+Version: 4.5.2
+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
+License: MIT
+Project-URL: Homepage, https://github.com/IronAdamant/wikifier
+Project-URL: Repository, https://github.com/IronAdamant/wikifier
+Project-URL: Documentation, https://github.com/IronAdamant/wikifier#readme
+Project-URL: Bug Tracker, https://github.com/IronAdamant/wikifier/issues
+Keywords: wiki,documentation,llm,agent,mcp,codebase,health-matrix,zero-dependency,shell,token-efficient,autonomous,record-change,mark-green,agent-wiki,llm-tools,dependency-graph,monorepo
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Software Development :: Documentation
+Classifier: Topic :: Software Development :: Version Control
+Classifier: Topic :: Text Processing :: Markup :: Markdown
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Provides-Extra: mcp
+Requires-Dist: mcp>=1.0.0; extra == "mcp"
+Dynamic: license-file
+
+# Wikifier
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![PyPI version](https://img.shields.io/pypi/v/wikifier.svg)](https://pypi.org/project/wikifier/)
+[![GitHub Stars](https://img.shields.io/github/stars/IronAdamant/wikifier?style=social)](https://github.com/IronAdamant/wikifier/stargazers)
+
+**A zero-dependency codebase wiki for AI agents** — token-efficient maps so LLMs look things up instead of re-reading full sources.
+
+Wikifier is an **agent-to-agent** tool: it builds a living map of a project (health matrix, dependency graph, short file summaries) and agents keep that map current as they work. Humans can peek via a small dashboard; the product is the agent loop, not a general docs site or IDE.
+
+Works from small scripts to large monorepos (Python + JavaScript/TypeScript imports, barrels, cycles, incremental updates).
+
+## Why
+
+Context windows are finite. Re-reading a large file to answer “what is this and who depends on it?” wastes tokens.
+
+Wikifier keeps a small set of artifacts agents can query:
+
+| Artifact | Role |
+|----------|------|
+| `file_health.md` | 🟢 / 🟡 / 🔴 matrix — what to trust, what to fix first |
+| `library.md` | File tree, Mermaid dependency map, import tables, cycles + confidence |
+| `*.wiki.md` | Short per-file “what this is for” notes (agent-maintained) |
+| `journal/` | Semantic *why* trail from `record-change` |
+
+Lookup beats re-ingest. That’s the whole idea.
+
+## Quick start
+
+```bash
+pip install wikifier            # pure Python stdlib core — no runtime deps
+pip install wikifier[mcp]       # optional Model Context Protocol (MCP) server
+
+cd /path/to/your/project
+wikifier init
+wikifier update-maps            # dependency graph + library.md
+wikifier check-changes
+wikifier health --summary
+```
+
+Always set an explicit root for external trees:
+
+```bash
+WIKIFIER_PROJECT_ROOT=/abs/path/to/project wikifier check-changes
+```
+
+## Agent loop
+
+Full protocol: [`skills/run.md`](skills/run.md).
+
+```bash
+wikifier check-changes
+# prioritize 🔴 then 🟡 in file_health.md / pending_updates.md
+# ... edit source ...
+wikifier record-change "path/file.py" "why this changed"   # required
+# ... refresh that file’s wiki summary ...
+wikifier mark-green "path/file.py"
+wikifier update-maps            # if imports/structure changed
+```
+
+`record-change` logs intent a git diff can’t reconstruct for the next agent (or human).
+
+## What you get
+
+- **Import analysis** — Python + JS/TS (ESM, CommonJS, dynamic imports, path aliases, package exports); per-edge confidence; name-routed barrel expansion (precise leaves, not edge explosion)
+- **Incremental pipeline** — pure-Python `update-maps`: dirty parse → import cache → reverse deps → cycles → `library.md`
+- **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 (`get_project_status`, `get_dependencies`, `get_file_wiki`, `record_change`, …)
+- **Zero core dependencies** — stdlib only; forks can add their own stack on top
+
+## 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 |
+
+Tests: `python -m unittest discover tests` (stdlib only).
+
+## Commands
+
+| Command | Purpose |
+|---------|---------|
+| `wikifier init [--target DIR]` | Bootstrap project + human `index.html` |
+| `wikifier check-changes` | Incremental scan → health / pending |
+| `wikifier record-change <file> "reason"` | Log *why* (required after edits) |
+| `wikifier mark-green <file>` | Mark wiki current |
+| `wikifier update-maps [--directory=src/] [--max-files=N]` | Rebuild graph + `library.md` |
+| `wikifier health [--summary\|--json]` | Health matrix (machine-friendly flags) |
+| `wikifier cycles` | Circular deps + break hints |
+| `wikifier monitor` / `daemon` | Background maintenance |
+| `wikifier serve` | Localhost dashboard with Run/Stop |
+
+Library: `from wikifier import check_changes, record_change, mark_green, health, update_maps`.
+
+## MCP
+
+```bash
+WIKIFIER_PROJECT_ROOT=/abs/path/to/project wikifier-mcp
+# or: python3 -m wikifier.mcp.server
+```
+
+Setup and tool list: [`wikifier/mcp/README.md`](wikifier/mcp/README.md).
+
+## Human dashboard (secondary)
+
+![Wikifier dashboard — file tree, health pills, local Run/Stop](https://raw.githubusercontent.com/IronAdamant/wikifier/main/screenshot/front_page_review.png)
+
+`wikifier init` drops a single `index.html`. Prefer **`wikifier serve`** (e.g. http://localhost:8787/index.html) — `file://` can’t load project files. The markdown artifacts and CLI/MCP tools stay the source of truth; the UI is a read-only window.
+
+## Scope
+
+**In:** agent-maintained codebase wiki, dependency intelligence, token-saving lookup for LLMs and coding agents.  
+**Out:** general human documentation systems, IDE plugins, “docs for everyone” product growth.
+
+## Links
+
+- [PyPI](https://pypi.org/project/wikifier/) · [GitHub](https://github.com/IronAdamant/wikifier)
+- Agent protocol: [`skills/run.md`](skills/run.md)
+- Changelog: [`CHANGELOG.md`](CHANGELOG.md)
+- Dogfood notes: `Findings/`

wikifier-4.5.2/README.md

@@ -0,0 +1,122 @@
+# Wikifier
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![PyPI version](https://img.shields.io/pypi/v/wikifier.svg)](https://pypi.org/project/wikifier/)
+[![GitHub Stars](https://img.shields.io/github/stars/IronAdamant/wikifier?style=social)](https://github.com/IronAdamant/wikifier/stargazers)
+
+**A zero-dependency codebase wiki for AI agents** — token-efficient maps so LLMs look things up instead of re-reading full sources.
+
+Wikifier is an **agent-to-agent** tool: it builds a living map of a project (health matrix, dependency graph, short file summaries) and agents keep that map current as they work. Humans can peek via a small dashboard; the product is the agent loop, not a general docs site or IDE.
+
+Works from small scripts to large monorepos (Python + JavaScript/TypeScript imports, barrels, cycles, incremental updates).
+
+## Why
+
+Context windows are finite. Re-reading a large file to answer “what is this and who depends on it?” wastes tokens.
+
+Wikifier keeps a small set of artifacts agents can query:
+
+| Artifact | Role |
+|----------|------|
+| `file_health.md` | 🟢 / 🟡 / 🔴 matrix — what to trust, what to fix first |
+| `library.md` | File tree, Mermaid dependency map, import tables, cycles + confidence |
+| `*.wiki.md` | Short per-file “what this is for” notes (agent-maintained) |
+| `journal/` | Semantic *why* trail from `record-change` |
+
+Lookup beats re-ingest. That’s the whole idea.
+
+## Quick start
+
+```bash
+pip install wikifier            # pure Python stdlib core — no runtime deps
+pip install wikifier[mcp]       # optional Model Context Protocol (MCP) server
+
+cd /path/to/your/project
+wikifier init
+wikifier update-maps            # dependency graph + library.md
+wikifier check-changes
+wikifier health --summary
+```
+
+Always set an explicit root for external trees:
+
+```bash
+WIKIFIER_PROJECT_ROOT=/abs/path/to/project wikifier check-changes
+```
+
+## Agent loop
+
+Full protocol: [`skills/run.md`](skills/run.md).
+
+```bash
+wikifier check-changes
+# prioritize 🔴 then 🟡 in file_health.md / pending_updates.md
+# ... edit source ...
+wikifier record-change "path/file.py" "why this changed"   # required
+# ... refresh that file’s wiki summary ...
+wikifier mark-green "path/file.py"
+wikifier update-maps            # if imports/structure changed
+```
+
+`record-change` logs intent a git diff can’t reconstruct for the next agent (or human).
+
+## What you get
+
+- **Import analysis** — Python + JS/TS (ESM, CommonJS, dynamic imports, path aliases, package exports); per-edge confidence; name-routed barrel expansion (precise leaves, not edge explosion)
+- **Incremental pipeline** — pure-Python `update-maps`: dirty parse → import cache → reverse deps → cycles → `library.md`
+- **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 (`get_project_status`, `get_dependencies`, `get_file_wiki`, `record_change`, …)
+- **Zero core dependencies** — stdlib only; forks can add their own stack on top
+
+## 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 |
+
+Tests: `python -m unittest discover tests` (stdlib only).
+
+## Commands
+
+| Command | Purpose |
+|---------|---------|
+| `wikifier init [--target DIR]` | Bootstrap project + human `index.html` |
+| `wikifier check-changes` | Incremental scan → health / pending |
+| `wikifier record-change <file> "reason"` | Log *why* (required after edits) |
+| `wikifier mark-green <file>` | Mark wiki current |
+| `wikifier update-maps [--directory=src/] [--max-files=N]` | Rebuild graph + `library.md` |
+| `wikifier health [--summary\|--json]` | Health matrix (machine-friendly flags) |
+| `wikifier cycles` | Circular deps + break hints |
+| `wikifier monitor` / `daemon` | Background maintenance |
+| `wikifier serve` | Localhost dashboard with Run/Stop |
+
+Library: `from wikifier import check_changes, record_change, mark_green, health, update_maps`.
+
+## MCP
+
+```bash
+WIKIFIER_PROJECT_ROOT=/abs/path/to/project wikifier-mcp
+# or: python3 -m wikifier.mcp.server
+```
+
+Setup and tool list: [`wikifier/mcp/README.md`](wikifier/mcp/README.md).
+
+## Human dashboard (secondary)
+
+![Wikifier dashboard — file tree, health pills, local Run/Stop](https://raw.githubusercontent.com/IronAdamant/wikifier/main/screenshot/front_page_review.png)
+
+`wikifier init` drops a single `index.html`. Prefer **`wikifier serve`** (e.g. http://localhost:8787/index.html) — `file://` can’t load project files. The markdown artifacts and CLI/MCP tools stay the source of truth; the UI is a read-only window.
+
+## Scope
+
+**In:** agent-maintained codebase wiki, dependency intelligence, token-saving lookup for LLMs and coding agents.  
+**Out:** general human documentation systems, IDE plugins, “docs for everyone” product growth.
+
+## Links
+
+- [PyPI](https://pypi.org/project/wikifier/) · [GitHub](https://github.com/IronAdamant/wikifier)
+- Agent protocol: [`skills/run.md`](skills/run.md)
+- Changelog: [`CHANGELOG.md`](CHANGELOG.md)
+- Dogfood notes: `Findings/`

{wikifier-4.5.0 → wikifier-4.5.2}/skills/run.md

@@ -2,11 +2,13 @@
 
 **Formerly "Wikifier Skills & Commands". This is the authoritative, versioned specification for agent behavior when using Wikifier.**
 
-**Version**: v0.6 (v4.2.0 real-pipeline + reliability update)  
-**Date**: 2026-06-10  
+**Version**: v0.6 (v4.2.0 real-pipeline + reliability update; package current **4.5.x**)  
+**Date**: 2026-06-10 (package notes refreshed 2026-07-09)  
 **Status**: Active. Supersedes v0.5.  
 **See also**: `README.md` (Intended Use section: strictly agent-to-agent wiki for token saving), M5-Dogfood-Assessment-Report.md, Findings/2026-06-10-Dogfood-Refactor-Validation.md, and the library in wikifier/.
 
+**Package 4.5.x notes (additive; protocol still v0.6):** File Tree as primary structure view in `library.md` + dashboard pan/zoom graph; `wikifier serve` with real Run/Stop controls; Python parser no longer leaks `#`-comment text into edges; MCP `get_project_status` / `get_files_needing_attention` use library+emoji health statuses (not legacy `[GREEN]` tags). Full history: `CHANGELOG.md`.
+
 **v0.6 migration notes (packages v4.2.0–v4.3.0)** — changes are additive or strictly-better defaults; v0.5 agent behavior keeps working:
 - `update-maps` (CLI) now runs the **pure-Python full pipeline**: every dirty file is parsed in-process, the canonical per-file cache is persisted, reverse deps + cycles + ACS are computed, and `library.md` is regenerated atomically. `--python-primary` is accepted but redundant; the in-shell first-pass was retired entirely (wikifier.sh's update-maps delegates to this pipeline; `--sh`/`--legacy-sh` are deprecated no-ops). Scoping is explicit via `--directory=`/`--max-files=` and reported in the result (`files_skipped`) — there are no silent caps.
 - `run_full_update`/`update_maps` returns gained additive fields: `files_parsed` (actual), `parseable_files`, `edges_persisted`, `files_skipped`, `cycles`, `library`. Tolerate additive fields as always.

{wikifier-4.5.0 → wikifier-4.5.2}/wikifier/__init__.py

@@ -61,4 +61,4 @@ from .contracts import (
     compute_acs_confidence,
 )
 
-__version__ = "4.5.0"
+__version__ = "4.5.2"

{wikifier-4.5.0 → wikifier-4.5.2}/wikifier/cli.py

@@ -683,8 +683,17 @@ def main():
             filtered_argv.append(arg)
         i += 1
 
-    # Micro-step 2 (A2 CLI wiring): detect streaming UX flags after parsing
-    a2_flag_markers = ("--stream", "--stream=", "--resume", "--resume_token", "--max-time", "--max_time", "--progress", "--summary", "--partial", "--dir=", "--directory=", "--max-files", "--max_files", "--format", "--format=summary", "--format=stream")
+    # Micro-step 2 (A2 CLI wiring): detect streaming UX flags after parsing.
+    # --max-files / --directory are normal run_full_update scoping options and
+    # must NOT force the stream facade (agents expect batch JSON + files_skipped).
+    a2_flag_markers = (
+        "--stream", "--stream=",
+        "--resume", "--resume_token",
+        "--max-time", "--max_time",
+        "--progress",
+        "--partial",
+        "--format=stream",
+    )
     has_a2_ux_flags = any(any(a == m or a.startswith(m) for m in a2_flag_markers) for a in filtered_argv)
 
     if project_root:
@@ -710,6 +719,37 @@ def main():
             print(f"[wikifier] health --{fmt} failed: {e}", file=sys.stderr)
             return 1
 
+    # Mandatory workflow commands: pure-Python primary (updates file_health.json + md).
+    # Shell upsert_health only patches the .md and on macOS `realpath --relative-to`
+    # is unavailable, so it used to store absolute paths as health keys.
+    if filtered_argv:
+        _cmd0 = filtered_argv[0].replace("_", "-")
+        _args = filtered_argv[1:]
+        try:
+            if _cmd0 == "check-changes":
+                res = check_changes(project_root=project_root)
+                n = int(res.get("changes_detected") or 0)
+                print("[wikifier] Running incremental change detection...")
+                if n:
+                    print(f"[wikifier] Detected {n} changed file(s). See pending_updates.md and file_health.md.")
+                else:
+                    print("[wikifier] No new changes detected.")
+                if res.get("message"):
+                    print(res["message"])
+                return 0 if res.get("success", True) else 1
+            if _cmd0 == "record-change" and len(_args) >= 2:
+                res = record_change(_args[0], " ".join(_args[1:]), project_root=project_root)
+                print(res.get("message") or res)
+                return 0 if res.get("success") else 1
+            if _cmd0 == "mark-green" and len(_args) >= 1:
+                reason = " ".join(_args[1:]) if len(_args) > 1 else ""
+                res = mark_green(_args[0], reason, project_root=project_root)
+                print(res.get("message") or res)
+                return 0 if res.get("success") else 1
+        except Exception as e:
+            print(f"[wikifier] Python-primary {_cmd0} failed: {e}", file=sys.stderr)
+            return 1
+
     # Human sub-project: ensure dashboards are in the target (for MCP + human investigation)
     # index.html = clean human view (chart + files + descriptions + copies); diagnostics.html for technical depth. Works alongside agent MCP/CLI use. No effect on agent SSOT or tools.
     if project_root:

{wikifier-4.5.0 → wikifier-4.5.2}/wikifier/mcp/server.py

@@ -643,7 +643,8 @@ def health(
     root = _get_effective_root(project_root)
 
     try:
-        import wikifier.health as health_module
+        import importlib
+        health_module = importlib.import_module("wikifier.health")
 
         if format == "summary":
             summary = health_module.get_summary(root, directory)
@@ -744,7 +745,8 @@ def list_healable_stubs(
     """
     root = _get_effective_root(project_root)
     try:
-        import wikifier.health as health_module
+        import importlib
+        health_module = importlib.import_module("wikifier.health")
         candidates = health_module.get_healable_stubs(
             root, min_wiki_length=min_wiki_length, directory=directory
         )
@@ -793,7 +795,8 @@ def heal_stubs(
     """
     root = _get_effective_root(project_root)
     try:
-        import wikifier.health as health_module
+        import importlib
+        health_module = importlib.import_module("wikifier.health")
         count = health_module.heal_outdated_stubs(
             root, min_wiki_length=min_wiki_length, dry_run=dry_run
         )
@@ -1571,13 +1574,15 @@ def get_files_needing_attention(
     root = _get_effective_root(project_root)
 
     try:
-        import wikifier.health as health_module
+        import importlib
+        health_module = importlib.import_module("wikifier.health")
 
+        # Health matrix stores emoji statuses (🟢/🟡/🔴), not [RED]/[YELLOW] tags.
         status_filter = None
         if status == "red":
-            status_filter = "[RED]"
+            status_filter = "🔴"
         elif status == "yellow":
-            status_filter = "[YELLOW]"
+            status_filter = "🟡"
 
         files = health_module.get_files_needing_attention(root, status_filter, directory)
 
@@ -1604,25 +1609,30 @@ def get_files_needing_attention(
         if not files:
             return "No files currently need attention."
 
-        red = [f for f in files if "[RED]" in f]  # This won't work well since we only have paths
-        # Better: we don't have status here easily. Let's just list them.
         return "Files needing attention:\n" + "\n".join(f"- {f}" for f in files)
 
     except Exception:
-        # Fallback
+        # Library fallback — avoid shell text parsing ([RED] tags vs emoji).
         root = _get_effective_root(project_root)
-        output = _run_wikifier_command("health", root=root)
-        lines = []
-        for line in output.splitlines():
-            if "[RED]" in line or "[YELLOW]" in line:
-                if directory and not line.strip().startswith(f"| {directory}"):
-                    continue
-                if status == "red" and "[RED]" not in line:
-                    continue
-                if status == "yellow" and "[YELLOW]" not in line:
-                    continue
-                lines.append(line.strip())
-        return "\n".join(lines) if lines else "No files currently need attention."
+        try:
+            import importlib
+            health_module = importlib.import_module("wikifier.health")
+            status_filter = "🔴" if status == "red" else ("🟡" if status == "yellow" else None)
+            files = health_module.get_files_needing_attention(root, status_filter, directory)
+            if format == "json":
+                return {
+                    "project_root": str(root),
+                    "directory": directory or ".",
+                    "status_filter": status,
+                    "files": files,
+                    "count": len(files),
+                    "acs_low_conf_context": None,
+                }
+            if not files:
+                return "No files currently need attention."
+            return "Files needing attention:\n" + "\n".join(f"- {f}" for f in files)
+        except Exception:
+            return "No files currently need attention."
 
 
 @mcp.tool()
@@ -1638,7 +1648,8 @@ def get_project_status(
     root = _get_effective_root(project_root)
 
     try:
-        import wikifier.health as health_module
+        import importlib
+        health_module = importlib.import_module("wikifier.health")
         summary = health_module.get_summary(root, directory)
         pending = _read_file_safe("pending_updates.md", root=root)
 
@@ -1763,19 +1774,35 @@ Pending updates: {pending_count}
 Use get_files_needing_attention() for the actual list. Use get_cycles(analysis=True) + get_dependencies(format="json") for ACS confidence_explanation Recommendations."""
 
     except Exception:
-        # Fallback to shell + text parsing
+        # Prefer library summary over shell text parsing. Live health text uses
+        # emoji (🟢/🟡/🔴); counting legacy [GREEN]/[YELLOW]/[RED] tags always
+        # yielded zeros and lied to agents.
         root = _get_effective_root(project_root)
-        health = _run_wikifier_command("health", root=root)
         pending = _read_file_safe("pending_updates.md", root=root)
-
-        red = health.count("[RED]")
-        yellow = health.count("[YELLOW]")
-        green = health.count("[GREEN]")
         pending_count = len([l for l in pending.splitlines() if l.strip() and not l.startswith("#")])
+        green = yellow = red = total = 0
+        try:
+            import importlib
+            health_module = importlib.import_module("wikifier.health")
+            summary = health_module.get_summary(root, directory)
+            total = int(summary.get("total", 0) or 0)
+            green = int(summary.get("green", 0) or 0)
+            yellow = int(summary.get("yellow", 0) or 0)
+            red = int(summary.get("red", 0) or 0)
+        except Exception:
+            # Last resort: emoji-aware (+ legacy tag) counts from health text.
+            try:
+                health_text = _run_wikifier_command("health", root=root)
+                green = health_text.count("🟢") + health_text.count("[GREEN]")
+                yellow = health_text.count("🟡") + health_text.count("[YELLOW]")
+                red = health_text.count("🔴") + health_text.count("[RED]")
+                total = green + yellow + red
+            except Exception:
+                pass
 
         if format == "json":
             return ProjectHealthSummary(
-                total_files=green + yellow + red,
+                total_files=total or (green + yellow + red),
                 green=green,
                 yellow=yellow,
                 red=red,
@@ -1884,7 +1911,8 @@ def suggest_next_actions(
     root = _get_effective_root(project_root)
 
     try:
-        import wikifier.health as health_module
+        import importlib
+        health_module = importlib.import_module("wikifier.health")
         summary = health_module.get_summary(root, directory)
         red = summary["red"]
         yellow = summary["yellow"]

{wikifier-4.5.0 → wikifier-4.5.2}/wikifier/parsers/javascript.py

@@ -938,7 +938,21 @@ def _follow_reexports(
         if target_module.startswith('.'):
             level = len(re.match(r'\.+', target_module).group())
             resolved = _resolve_relative_import(current_file, target_module, level)
-            resolved_path = _try_resolve_relative_path(current_file, target_module)
+            # Prefer central_resolve directly (R4); avoid the deprecated shim on the
+            # hot path so tests/production do not emit DeprecationWarning.
+            resolved_path = None
+            try:
+                if central_resolve is not None:
+                    proj_root = _get_project_root_fallback(current_file.parent)
+                    r = central_resolve(target_module, str(current_file), proj_root)
+                    resolved_path = r.resolved_file
+            except Exception:
+                resolved_path = None
+            if not resolved_path:
+                # Silent legacy FS fallthrough (same body as deprecated shim tail).
+                with warnings.catch_warnings():
+                    warnings.simplefilter("ignore", DeprecationWarning)
+                    resolved_path = _try_resolve_relative_path(current_file, target_module)
             if not resolved_path:
                 return [{
                     "module": resolved,

{wikifier-4.5.0 → wikifier-4.5.2}/wikifier/scripts/wikifier.sh

@@ -149,6 +149,29 @@ build_exclude_expr() {
     fi
 }
 
+# Build find(1) exclude arguments from exclude_patterns.txt as a bash array.
+# The string form from build_exclude_expr embeds literal quote characters and
+# cannot be expanded safely into a find command without eval; this array form
+# is what scan commands (check-changes, validate) must use.
+EXCLUDE_FIND_ARGS=()
+build_exclude_find_args() {
+    EXCLUDE_FIND_ARGS=()
+    [[ -f "$EXCLUDE_PATTERNS_FILE" ]] || return 0
+    local pat
+    local parts=()
+    while IFS= read -r pat; do
+        [[ -z "$pat" || "$pat" =~ ^[[:space:]]*# ]] && continue
+        pat=$(echo "$pat" | xargs)
+        [[ -z "$pat" ]] && continue
+        if ((${#parts[@]})); then parts+=(-o); fi
+        # dir-name patterns prune contents; -name catches file globs (*.pyc) and exact basenames
+        parts+=(-path "*/$pat/*" -o -path "*/$pat" -o -name "$pat")
+    done < "$EXCLUDE_PATTERNS_FILE"
+    if ((${#parts[@]})); then
+        EXCLUDE_FIND_ARGS=('!' '(' "${parts[@]}" ')')
+    fi
+}
+
 # Upsert a row in the Markdown health table (very simple but effective)
 # We treat file_health.md as the single source of truth.
 upsert_health() {
@@ -298,8 +321,7 @@ cmd_check_changes() {
         echo "$last_ts" > "$LAST_CHECK_FILE"
     fi
 
-    local exclude
-    exclude=$(build_exclude_expr)
+    build_exclude_find_args
 
     local changed=0
     local changed_files_list=""
@@ -309,7 +331,6 @@ cmd_check_changes() {
         [[ -z "$root" ]] && continue
         [[ ! -e "$root" ]] && { log "Warning: monitored path does not exist: $root"; continue; }
 
-        # shellcheck disable=SC2086
         while IFS= read -r -d '' file; do
             # Skip the wikifier tool's own internal files
             if [[ "$file" == *"/.wikifier_staging/"* || "$file" == *"/journal/"* || \
@@ -317,8 +338,16 @@ cmd_check_changes() {
                 continue
             fi
 
+            # Portable project-relative path. GNU realpath --relative-to is not on
+            # macOS BSD realpath; falling back to the absolute path polluted health
+            # keys (and shell upsert only patched .md, not file_health.json).
             local rel_file
-            rel_file=$(realpath --relative-to="$PROJECT_ROOT" "$file" 2>/dev/null || echo "$file")
+            case "$file" in
+                "$PROJECT_ROOT"/*) rel_file="${file#"$PROJECT_ROOT"/}" ;;
+                *)
+                    rel_file=$(python3 -c "from pathlib import Path; import sys; print(Path(sys.argv[1]).resolve().relative_to(Path(sys.argv[2]).resolve()))" "$file" "$PROJECT_ROOT" 2>/dev/null || echo "$file")
+                    ;;
+            esac
 
             upsert_health "$rel_file" "🟡 Yellow" "mtime changed since last check-changes (auto-detected)"
             # Collect for delta barrel reports (Wave continuation: pass changed list to BRC get_reports for O(changed) + rich auto-Yellow only on relevant)
@@ -327,7 +356,7 @@ cmd_check_changes() {
             write_journal "auto-detected" "$rel_file" "File mtime changed (check-changes)"
 
             changed=$((changed + 1))   # set -e safe (((changed++)) returns 1 at 0)
-        done < <(find "$root" -type f -newermt "$last_ts" -print0 2>/dev/null || true)
+        done < <(find "$root" -type f ${EXCLUDE_FIND_ARGS[@]+"${EXCLUDE_FIND_ARGS[@]}"} -newermt "$last_ts" -print0 2>/dev/null || true)
     done < <(get_monitored_paths)
 
     date '+%Y-%m-%d %H:%M:%S' > "$LAST_CHECK_FILE"
@@ -550,14 +579,18 @@ cmd_validate() {
     log "Validating that every monitored file has a health entry..."
 
     local missing=0
-    local exclude
-    exclude=$(build_exclude_expr)
+    build_exclude_find_args
 
     while IFS= read -r root; do
         [[ -z "$root" ]] && continue
-        find "$root" -type f ! -path "*/.git/*" ! -path "*/.wikifier_staging/*" 2>/dev/null | while read -r f; do
+        find "$root" -type f ! -path "*/.git/*" ! -path "*/.wikifier_staging/*" ${EXCLUDE_FIND_ARGS[@]+"${EXCLUDE_FIND_ARGS[@]}"} 2>/dev/null | while read -r f; do
             local rel
-            rel=$(realpath --relative-to="$PROJECT_ROOT" "$f" 2>/dev/null || echo "$f")
+            case "$f" in
+                "$PROJECT_ROOT"/*) rel="${f#"$PROJECT_ROOT"/}" ;;
+                *)
+                    rel=$(python3 -c "from pathlib import Path; import sys; print(Path(sys.argv[1]).resolve().relative_to(Path(sys.argv[2]).resolve()))" "$f" "$PROJECT_ROOT" 2>/dev/null || echo "$f")
+                    ;;
+            esac
             if ! grep -qF "| $rel |" "$FILE_HEALTH" 2>/dev/null; then
                 echo "🔴 MISSING WIKI ENTRY: $rel"
                 ((missing++)) || true