Add security hardening, Ghidra, recreate skill, checkpoints, shells, web search and themes

- Sandbox (bubblewrap) for non-admin shell/git, MCP per-user rights, hard budgets and quotas,
  login rate limiting, audit log and backups
- Ghidra headless decompilation (ARM64 natives built from source), binary_info tool,
  clean room / deep workflow per session
- Recreate skill and commands for analysing and re-building old software
- File checkpoints with rewind/restore, background shells (bash_output, kill_shell)
- web_search tool (DuckDuckGo, SearXNG, Brave, Tavily)
- In-app dialogs and toasts instead of browser dialogs
- 15 base themes (trilium-themes palettes plus Nord, VS Code, GitHub, Catppuccin, One,
  Dracula, Rose Pine, Everforest, Kanagawa) with light/dark/auto switcher and license notes

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

server/src/tools/fs.rs

@@ -46,6 +46,8 @@ impl Tool for Read {
     fn description(&self) -> String {
         "Read a file. Returns numbered lines (cat -n style). Use offset/limit for large files \
          (default: first 2000 lines). Images (png, jpg, gif, webp) are returned as images. \
+         Documents are converted to text: PDF (pages=\"3-7\", scanned pages come as images), \
+         Excel/ODS spreadsheets (sheet=\"Name\"), Word .docx and PowerPoint .pptx. \
          Always read a file before editing or overwriting it."
             .into()
     }
@@ -55,7 +57,9 @@ impl Tool for Read {
             "properties": {
                 "path": {"type": "string", "description": "File path, absolute or relative to the working directory"},
                 "offset": {"type": "integer", "description": "1-based line to start from"},
-                "limit": {"type": "integer", "description": "Number of lines to read"}
+                "limit": {"type": "integer", "description": "Number of lines to read"},
+                "pages": {"type": "string", "description": "PDF only: page or range, e.g. \"2-5\""},
+                "sheet": {"type": "string", "description": "Spreadsheets only: sheet name"}
             },
             "required": ["path"]
         })
@@ -67,10 +71,15 @@ impl Tool for Read {
         format!("Read {}", input["path"].as_str().unwrap_or("?"))
     }
     async fn run(&self, input: Value, ctx: &ToolCtx) -> Result<ToolOutput> {
-        let path = ctx.resolve(arg_str(&input, "path")?)?;
+        let path = ctx.resolve_read(arg_str(&input, "path")?)?;
         if path.is_dir() {
             bail!("{} is a directory – use the list tool", path.display());
         }
+        if crate::docs::is_document(&path) {
+            ctx.app.mark_read(&ctx.session_id, &path);
+            let (text, images) = crate::docs::extract(&path, input["pages"].as_str(), input["sheet"].as_str()).await?;
+            return Ok(ToolOutput { content: truncate(&text, MAX_OUTPUT * 2), images, ..Default::default() });
+        }
         let bytes = tokio::fs::read(&path).await?;
         ctx.app.mark_read(&ctx.session_id, &path);
         if let Some(mt) = image_type(&path) {
@@ -273,7 +282,7 @@ impl Tool for List {
         true
     }
     async fn run(&self, input: Value, ctx: &ToolCtx) -> Result<ToolOutput> {
-        let dir = ctx.resolve(input["path"].as_str().unwrap_or("."))?;
+        let dir = ctx.resolve_read(input["path"].as_str().unwrap_or("."))?;
         let depth = input["depth"].as_u64().unwrap_or(1).clamp(1, 5) as usize;
         let cwd = ctx.cwd.clone();
         let out = tokio::task::spawn_blocking(move || {
@@ -328,7 +337,7 @@ impl Tool for Glob {
     }
     async fn run(&self, input: Value, ctx: &ToolCtx) -> Result<ToolOutput> {
         let pattern = arg_str(&input, "pattern")?.to_string();
-        let root = ctx.resolve(input["path"].as_str().unwrap_or("."))?;
+        let root = ctx.resolve_read(input["path"].as_str().unwrap_or("."))?;
         let out = tokio::task::spawn_blocking(move || -> Result<String> {
             let matcher = globset::GlobBuilder::new(&pattern).literal_separator(true).build()?.compile_matcher();
             let mut hits = Vec::new();
@@ -394,7 +403,7 @@ impl Tool for Grep {
         let re = regex::RegexBuilder::new(arg_str(&input, "pattern")?)
             .case_insensitive(input["case_insensitive"].as_bool().unwrap_or(false))
             .build()?;
-        let root = ctx.resolve(input["path"].as_str().unwrap_or("."))?;
+        let root = ctx.resolve_read(input["path"].as_str().unwrap_or("."))?;
         let glob = input["glob"]
             .as_str()
             .map(|g| globset::Glob::new(g).map(|g| g.compile_matcher()))