Scanner silently omits symlinked markdown files (and other unreadable entries) from the tree

[anbturki]

Summary

A symlinked .md file inside a workspace never appears in the tree: the scanner walks with follow_links(false) and then requires file_type().is_file(), which is false for symlinks, so the entry is dropped without any indication. The same silent-omission pattern applies to permission-denied subtrees and files over the 4 MiB cap.

Reproduction (release build of f485396, macOS)

1. In a scanned workspace, run ln -s ~/outside-doc.md research/linked-from-outside.md and create research/visible-control.md in the same batch.
2. Wait for the watcher rescan: the control appears, the symlink never does (screenshot from the same session as issue Docs under a phase folder named build, dist, target, or venv are permanently invisible in the GUI #20: "5 files", no linked-from-outside entry despite the symlink existing on disk).

Root cause

• src-tauri/core/src/scan.rs:154: follow_links(false); scan.rs:184-186: non-regular files (including symlinks) skipped.
• Same class of silent omissions, none of which set the truncated flag or surface anywhere:
  • walker.filter_map(|e| e.ok()) at scan.rs:168 drops permission-denied subtrees wholesale.
  • entry.metadata().ok()? / read_partial(...).ok()? at scan.rs:212, 220 drop unreadable files.
  • Files larger than 4 MiB are skipped (scan.rs:18, 193-197) without being counted or reported. MCP writes are capped at the same limit, so only files written by other tools hit this.

Proposed fix

Follow symlinks to regular files (with a cycle guard, or at minimum resolve and include link targets that are files), and count skipped/unreadable entries so the UI can say "N files skipped" instead of silently presenting a partial tree.

Screenshot

Symlink research/linked-from-outside.md exists on disk but is absent from the tree (control file from the same batch is present):

[anbturki]

Fixed by following symlinks when scanning (walkdir's loop detection reports cycles as errors) and counting walker errors, unreadable files, and oversize files into a new skipped count shown in the explorer footer. Verified live: a symlinked doc now appears in the tree.

Shipped in v0.9.1 (PR #24, commit 30b329e). The macOS build is notarized and stapled; downloads are on the release page.