From 0d2c16172fceb97deb8db1b320620452edc0cd0d Mon Sep 17 00:00:00 2001
From: Research Assistant <research@example.com>
Date: Tue, 28 Apr 2026 23:58:02 +0800
Subject: [PATCH] fix: correct UPDATEABLE_PATHS repo paths; plugin install uses
 vault-first source; exclude table images from figure-map matching

---
 paperforge/__init__.py                        |  2 +-
 .../skills/literature-qa/scripts/ld_deep.py   | 16 +++++++++++---
 paperforge/worker/status.py                   |  2 +-
 paperforge/worker/update.py                   | 22 ++++++++++++-------
 4 files changed, 29 insertions(+), 13 deletions(-)

diff --git a/paperforge/__init__.py b/paperforge/__init__.py
index d683afaa..9f405238 100644
--- a/paperforge/__init__.py
+++ b/paperforge/__init__.py
@@ -1,3 +1,3 @@
 """paperforge — PaperForge package."""
 
-__version__ = "1.4.5"
+__version__ = "1.4.6"
diff --git a/paperforge/skills/literature-qa/scripts/ld_deep.py b/paperforge/skills/literature-qa/scripts/ld_deep.py
index daaa1cc8..18734a9b 100644
--- a/paperforge/skills/literature-qa/scripts/ld_deep.py
+++ b/paperforge/skills/literature-qa/scripts/ld_deep.py
@@ -699,17 +699,27 @@ def build_figure_map(fulltext: str, zotero_key: str = "") -> dict:
             caption_text = m.group(2).strip() if len(m.groups()) > 1 else ""
 
             # Find nearest image within window of adjacent pages (current ± 2 pages)
+            # Filter: figure captions → exclude table images; table captions → prefer table images
             best_image = None
             min_distance = float("inf")
+            is_table_type = entry_type in ("main_table", "supplementary_table")
 
             for img in all_images:
-                # Check if image is within 2 pages of current page
+                img_name_lower = img.get("link", "").lower()
+                img_is_table = "table" in img_name_lower
+
+                # Figure captions: skip images that are clearly table screenshots
+                if not is_table_type and img_is_table:
+                    continue
+
                 if current_page is not None and img["page"] is not None:
                     page_diff = abs(img["page"] - current_page)
                     if page_diff <= 2:
                         distance = abs(img["line_idx"] - idx)
-                        if distance < min_distance:
-                            min_distance = distance
+                        # Table captions: boost score for table images (+ priority)
+                        score = distance - 100 if (is_table_type and img_is_table) else distance
+                        if score < min_distance:
+                            min_distance = score
                             best_image = img
 
             # Find additional images on the same page near the best image
diff --git a/paperforge/worker/status.py b/paperforge/worker/status.py
index 640158ed..a1793139 100644
--- a/paperforge/worker/status.py
+++ b/paperforge/worker/status.py
@@ -498,4 +498,4 @@ def run_status(vault: Path, verbose: bool = False, json_output: bool = False) ->
 GITHUB_REPO = "LLLin000/PaperForge"
 GITHUB_ZIP = f"https://github.com/{GITHUB_REPO}/archive/refs/heads/master.zip"
 
-UPDATEABLE_PATHS = ["skills", "pipeline", "command", "scripts", "plugin"]
+UPDATEABLE_PATHS = ["command", "scripts", "paperforge/skills", "paperforge/plugin"]
diff --git a/paperforge/worker/update.py b/paperforge/worker/update.py
index 2ce65f9f..57bf1379 100644
--- a/paperforge/worker/update.py
+++ b/paperforge/worker/update.py
@@ -216,17 +216,23 @@ def update_via_zip(vault: Path) -> bool:
 
 
 def _install_obsidian_plugin(vault: Path) -> bool:
-    """Copy Obsidian plugin files into .obsidian/plugins/paperforge/."""
-    try:
-        import importlib
-        import paperforge
-        importlib.reload(paperforge)
+    """Copy Obsidian plugin files into .obsidian/plugins/paperforge/.
 
-        pkg_dir = Path(paperforge.__file__).parent.resolve()
-        plugin_src = pkg_dir / "plugin"
+    Source priority: vault copy (git/zip) → Python package (pip).
+    """
+    try:
         plugin_dst = vault / ".obsidian" / "plugins" / "paperforge"
 
-        if not plugin_src.exists() or not plugin_src.is_dir():
+        # Try vault copy first (works for git pull and zip updates)
+        plugin_src = vault / "paperforge" / "plugin"
+        if not plugin_src.is_dir():
+            # Fallback: Python package location (works for pip)
+            import importlib
+            import paperforge
+            importlib.reload(paperforge)
+            plugin_src = Path(paperforge.__file__).parent.resolve() / "plugin"
+
+        if not plugin_src.is_dir():
             logger.warning("Plugin source not found: %s", plugin_src)
             return False