chore: run-precommit on everything

Author: zah

.cspell.json

@@ -5,7 +5,9 @@
   "useGitignore": true,
   "ignorePaths": [
     "specs/Initial Developer Input/**",
-    "specs/Research/**"
+    "specs/Research/**",
+    "repomix.md",
+    ".obsidian/**"
   ],
   "words": [
     "Blocksense","zellij","devcontainers","sandboxed","preconfigured","agentic","triager",
@@ -20,6 +22,12 @@
     "tailscaled","Headscale","tailnet","bytestreams",
     "cachix","sccache","GOPATH","ccache","substituters","pipx","ZDOTDIR","OPENROUTER","tini","WCAG","automations",
     "scriptable","Rakefile","Ilib","subvolumes","reflinks","lowerdir","upperdir","venv","MSYS","pytest","rescan","lockfiles","virtualenv","exfiltration",
-    "LOCALAPPDATA","AUTOINCREMENT","pijul"
+    "LOCALAPPDATA","AUTOINCREMENT","pijul",
+    "Sandboxing","pids","distro","userns","openat2","overlayfs","slirp","netns","nodev","nosuid","noexec","devpts","ptys","newinstance","GOCACHE","EACCES","EPERM","PTRACER","dumpable","veth","PRIVS","setuid","syscalls","kexec","tunables","DNAT","cgroupfs","netdev","securebits","privs","ADDFD","TOCTOU","fanotify","resolv",
+    "unshares","notif","NEWUSER","newuidmap","newgidmap","NEWNS","NEWPID","NEWUTS","NEWIPC","NEWTIME","NEWNET","hidepid","ptmxmode","urandom","ptmx","setattr","RDONLY","upperdirs","statx","fstatat","faccessat","execve","execveat","linkat","renameat","syscall","MAGICLINKS","NOTIF","errno","tracee","mmap","nftables","chowning","openat",
+    "exitstatus","autorun","mountpoint","rebornix","rdbg","popen","envgen","progname",
+    "tagxref","tagid","tagname","revset","objid","whatchanged","revno","mlink","fnid",
+    "DEVNULL","autosync","fslckout","hgrc","revid","autopush","EDQUOT","Repomix","optparse","hexdigest","mktmpdir","envrc","rubocop","Justfile","Shellwords","shellwords","gettime","nprocessors","pipefail","esac","elif","incovenient","Futhermore","dispay","Rubo","metacraft",
+    "pico","testuser","NOSYSTEM","ASKPASS","subvol","qgroup","Workstreams","binwrite","extensionless","choco","Itest","mswin"
   ]
 }

.devcontainer/scripts/efficient-copy.sh

@@ -18,64 +18,64 @@ set -euo pipefail
 #   $2 - Destination directory path
 #   $3 - Optional: --verbose for detailed output
 efficient_copy() {
-    local source_dir="$1"
-    local dest_dir="$2"
-    local verbose=false
+  local source_dir="$1"
+  local dest_dir="$2"
+  local verbose=false
 
-    # Parse optional verbose flag
-    if [[ "${3:-}" == "--verbose" ]]; then
-        verbose=true
-    fi
+  # Parse optional verbose flag
+  if [[ "${3:-}" == "--verbose" ]]; then
+    verbose=true
+  fi
 
-    # Validate source directory exists and is not empty
-    if [[ ! -d "$source_dir" ]] || [[ -z "$(ls -A "$source_dir" 2>/dev/null)" ]]; then
-        [[ "$verbose" == true ]] && echo "Source directory '$source_dir' doesn't exist or is empty"
-        return 1
-    fi
+  # Validate source directory exists and is not empty
+  if [[ ! -d "$source_dir" ]] || [[ -z "$(ls -A "$source_dir" 2>/dev/null)" ]]; then
+    [[ "$verbose" == true ]] && echo "Source directory '$source_dir' doesn't exist or is empty"
+    return 1
+  fi
 
-    # Ensure destination directory exists
-    if ! mkdir -p "$dest_dir"; then
-        [[ "$verbose" == true ]] && echo "Failed to create destination directory '$dest_dir'"
-        return 2
-    fi
+  # Ensure destination directory exists
+  if ! mkdir -p "$dest_dir"; then
+    [[ "$verbose" == true ]] && echo "Failed to create destination directory '$dest_dir'"
+    return 2
+  fi
 
-    # Strategy 1: Copy-on-write (fastest, zero disk usage until modification)
-    if command -v cp >/dev/null 2>&1 && cp --help 2>/dev/null | grep -q "\--reflink"; then
-        [[ "$verbose" == true ]] && echo "Attempting copy-on-write..."
-        if cp -r --reflink=auto "$source_dir"/* "$dest_dir/" 2>/dev/null; then
-            [[ "$verbose" == true ]] && echo "✓ Copy-on-write successful"
-            return 0
-        fi
-        [[ "$verbose" == true ]] && echo "✗ Copy-on-write failed, trying hard links..."
+  # Strategy 1: Copy-on-write (fastest, zero disk usage until modification)
+  if command -v cp >/dev/null 2>&1 && cp --help 2>/dev/null | grep -q "\--reflink"; then
+    [[ "$verbose" == true ]] && echo "Attempting copy-on-write..."
+    if cp -r --reflink=auto "$source_dir"/* "$dest_dir/" 2>/dev/null; then
+      [[ "$verbose" == true ]] && echo "✓ Copy-on-write successful"
+      return 0
     fi
+    [[ "$verbose" == true ]] && echo "✗ Copy-on-write failed, trying hard links..."
+  fi
 
-    # Strategy 2: Hard links (fast, space-efficient, same filesystem required)
-    if cp -rl "$source_dir"/* "$dest_dir/" 2>/dev/null; then
-        [[ "$verbose" == true ]] && echo "✓ Hard link copy successful"
-        return 0
-    fi
-    [[ "$verbose" == true ]] && echo "✗ Hard link copy failed, trying rsync..."
+  # Strategy 2: Hard links (fast, space-efficient, same filesystem required)
+  if cp -rl "$source_dir"/* "$dest_dir/" 2>/dev/null; then
+    [[ "$verbose" == true ]] && echo "✓ Hard link copy successful"
+    return 0
+  fi
+  [[ "$verbose" == true ]] && echo "✗ Hard link copy failed, trying rsync..."
 
-    # Strategy 3: Rsync with deduplication (good for incremental updates)
-    if command -v rsync >/dev/null 2>&1; then
-        if rsync -a --link-dest="$source_dir" "$source_dir"/ "$dest_dir/" 2>/dev/null; then
-            [[ "$verbose" == true ]] && echo "✓ Rsync copy successful"
-            return 0
-        fi
-        [[ "$verbose" == true ]] && echo "✗ Rsync failed, trying regular copy..."
+  # Strategy 3: Rsync with deduplication (good for incremental updates)
+  if command -v rsync >/dev/null 2>&1; then
+    if rsync -a --link-dest="$source_dir" "$source_dir"/ "$dest_dir/" 2>/dev/null; then
+      [[ "$verbose" == true ]] && echo "✓ Rsync copy successful"
+      return 0
     fi
+    [[ "$verbose" == true ]] && echo "✗ Rsync failed, trying regular copy..."
+  fi
 
-    # Strategy 4: Regular copy (slowest but most compatible)
-    if cp -r "$source_dir"/* "$dest_dir/" 2>/dev/null; then
-        [[ "$verbose" == true ]] && echo "✓ Regular copy successful"
-        return 0
-    fi
+  # Strategy 4: Regular copy (slowest but most compatible)
+  if cp -r "$source_dir"/* "$dest_dir/" 2>/dev/null; then
+    [[ "$verbose" == true ]] && echo "✓ Regular copy successful"
+    return 0
+  fi
 
-    [[ "$verbose" == true ]] && echo "✗ All copy methods failed"
-    return 3
+  [[ "$verbose" == true ]] && echo "✗ All copy methods failed"
+  return 3
 }
 
 # If script is executed directly (not sourced), call the function with arguments
 if [[ "${BASH_SOURCE[0]}" == "${0}" ]]; then
-    efficient_copy "$@"
+  efficient_copy "$@"
 fi

.devcontainer/scripts/setup-nix-substituters.sh

@@ -6,14 +6,14 @@
 
 # Check if we've already configured the substituters
 if grep -q "extra-substituters.*file:///nix/host-store" ~/.config/nix/nix.conf 2>/dev/null; then
-    # Already configured, exit silently
-    exit 0
+  # Already configured, exit silently
+  exit 0
 fi
 
 if [ -d "/nix/host-store" ] && [ "$(ls -A /nix/host-store 2>/dev/null)" ]; then
-    echo "Host Nix store detected, enabling substituter..."
-    echo "extra-substituters = file:///nix/host-store" >> ~/.config/nix/nix.conf
-    echo "trusted-substituters = file:///nix/host-store" >> ~/.config/nix/nix.conf
+  echo "Host Nix store detected, enabling substituter..."
+  echo "extra-substituters = file:///nix/host-store" >>~/.config/nix/nix.conf
+  echo "trusted-substituters = file:///nix/host-store" >>~/.config/nix/nix.conf
 else
-    echo "No host Nix store found, using container-only mode"
+  echo "No host Nix store found, using container-only mode"
 fi

.devcontainer/scripts/sync-cargo-caches.sh

@@ -15,35 +15,35 @@ mkdir -p "$CONTAINER_CARGO_HOME"/{bin,registry,git}
 
 # Sync host cache to container cache if available
 if [ -d "$HOST_CARGO_HOME" ] && [ "$(ls -A $HOST_CARGO_HOME 2>/dev/null)" ]; then
-    echo "Host Cargo cache detected, syncing with container cache..."
-
-    # Sync registry data using efficient copying utility
-    if [ -d "$HOST_CARGO_HOME/registry" ]; then
-        echo "Syncing registry cache (this may take a moment on first run)..."
-
-        # Execute the efficient copy utility as a standalone script
-        if "$SCRIPT_DIR/efficient-copy" "$HOST_CARGO_HOME/registry" "$CONTAINER_CARGO_HOME/registry" --verbose; then
-            echo "✓ Registry cache synced from host"
-
-            # Show some stats about what we have
-            if [ -d "$CONTAINER_CARGO_HOME/registry/cache" ]; then
-                cache_count=$(find "$CONTAINER_CARGO_HOME/registry/cache" -name "*.crate" 2>/dev/null | wc -l)
-                echo "  → $cache_count cached crate files available"
-            fi
-        else
-            echo "⚠ Warning: Failed to sync cache from host, using existing container cache"
-        fi
+  echo "Host Cargo cache detected, syncing with container cache..."
+
+  # Sync registry data using efficient copying utility
+  if [ -d "$HOST_CARGO_HOME/registry" ]; then
+    echo "Syncing registry cache (this may take a moment on first run)..."
+
+    # Execute the efficient copy utility as a standalone script
+    if "$SCRIPT_DIR/efficient-copy" "$HOST_CARGO_HOME/registry" "$CONTAINER_CARGO_HOME/registry" --verbose; then
+      echo "✓ Registry cache synced from host"
+
+      # Show some stats about what we have
+      if [ -d "$CONTAINER_CARGO_HOME/registry/cache" ]; then
+        cache_count=$(find "$CONTAINER_CARGO_HOME/registry/cache" -name "*.crate" 2>/dev/null | wc -l)
+        echo "  → $cache_count cached crate files available"
+      fi
+    else
+      echo "⚠ Warning: Failed to sync cache from host, using existing container cache"
     fi
+  fi
 
-    echo "Container cache is now up-to-date with host. New downloads will be stored in container."
+  echo "Container cache is now up-to-date with host. New downloads will be stored in container."
 else
-    echo "No host Cargo cache found, using container-only mode"
+  echo "No host Cargo cache found, using container-only mode"
 fi
 
 # Ensure Cargo configuration exists (idempotent)
 if [ ! -f "$CONTAINER_CARGO_HOME/config.toml" ]; then
-    echo "Setting up Cargo configuration..."
-    cat > "$CONTAINER_CARGO_HOME/config.toml" << 'EOF'
+  echo "Setting up Cargo configuration..."
+  cat >"$CONTAINER_CARGO_HOME/config.toml" <<'EOF'
 # Cargo configuration for container environment
 # Reference: https://doc.rust-lang.org/cargo/reference/config.html
 
@@ -55,9 +55,9 @@ git-fetch-with-cli = true
 # [build]
 # target-dir = "/tmp/cargo-target"
 EOF
-    echo "✓ Cargo configuration created"
+  echo "✓ Cargo configuration created"
 else
-    echo "✓ Cargo configuration already exists"
+  echo "✓ Cargo configuration already exists"
 fi
 
 echo "Development cache sync complete!"

.gitignore

@@ -9,3 +9,8 @@ test/logs/
 # linter cache
 .rubocop-cache/
 .pre-commit-config.yaml
+
+.cspellcache
+.lycheecache
+
+repomix.md

.obsidian/core-plugins.json

@@ -27,5 +27,7 @@
   "file-recovery": true,
   "publish": false,
   "sync": true,
-  "webviewer": false
+  "webviewer": false,
+  "footnotes": false,
+  "bases": true
 }

.obsidian/workspace.json

@@ -13,12 +13,22 @@
             "state": {
               "type": "markdown",
               "state": {
-                "file": "specs/Research/Sandboxing Technologies.md",
+                "file": "specs/Public/Sanboxing/Local Sandboxing on Linux.md",
                 "mode": "source",
-                "source": false
+                "source": false,
+                "backlinks": true,
+                "backlinkOpts": {
+                  "collapseAll": false,
+                  "extraContext": false,
+                  "sortOrder": "alphabetical",
+                  "showSearch": false,
+                  "searchQuery": "",
+                  "backlinkCollapsed": false,
+                  "unlinkedCollapsed": true
+                }
               },
               "icon": "lucide-file",
-              "title": "Sandboxing Technologies"
+              "title": "Local Sandboxing on Linux"
             }
           },
           {
@@ -184,6 +194,7 @@
   },
   "left-ribbon": {
     "hiddenItems": {
+      "bases:Create new base": false,
       "switcher:Open quick switcher": false,
       "graph:Open graph view": false,
       "canvas:Create new canvas": false,
@@ -194,13 +205,20 @@
   },
   "active": "01bf72509d2b5652",
   "lastOpenFiles": [
+    "lychee.toml",
+    "specs/Research/Restricting Guest Internet Access to a Whitelist of Websites.md",
+    "specs/Research/Supervisor Process for Dynamic File Access Control on Linux.md",
+    "specs/Research/fds.md",
+    "specs/Public/Sanboxing/Agents Workflow Sandboxing Strategies.md",
+    "specs/Public/Sanboxing/Local Sandboxing on Linux.md",
+    "specs/Research/Sandboxing Technologies.md",
+    "specs/Public/Sanboxing",
     "docs/state-persistence.md",
     "docs/marketing-one-pager.md",
     "docs/guide.md",
     "docs/AI Development Guide.md",
     "specs/Public/State Persistence.md",
     "docs/Product One Pager.md",
-    "specs/Research/Sandboxing Technologies.md",
     "specs/Public/CLI.md",
     "specs/Research/MicroVM Research.md",
     "specs/Public/Nix Devcontainer/Devcontainer Design.md",
@@ -215,12 +233,6 @@
     "specs/Public/Nix Devcontainer/Devcontainer Cache Guidelines.md",
     "specs/Public/FS Snapshots/FS Snapshots Overview.md",
     "specs/Public/Agent Browsers/Agent Browser Profiles.md",
-    "specs/Public/Browser Automation/Codex.md",
-    "specs/Public/Extras Framework.md",
-    "specs/Public/Lima VM Images.md",
-    "specs/Public/Agent Time Travel.md",
-    "specs/Public/WebUI PRD.md",
-    "specs/Public/TUI PRD.md",
     "specs/Public",
     "agent-task-0.1.0.gem",
     "test/logs/temp_output_20250828_001209.log",

.vale.ini

@@ -1,5 +1,5 @@
 # Minimal Vale configuration for repository Markdown
-MinAlertLevel = warning
+MinAlertLevel = error
 
 StylesPath = .vale
 Vocab = AgentsWorkflow
@@ -8,3 +8,5 @@ Vocab = AgentsWorkflow
 BasedOnStyles = Vale
 Vale.Spelling = YES
 Vale.Terms = NO
+
+ 

.vale/Vale/Spelling.yml

@@ -0,0 +1,35 @@
+extends: spelling
+message: "Did you really mean '%s'?"
+level: warning
+ignore:
+  - Blocksense
+  - sandboxed
+  - Sandboxing
+  - GUIs
+  - namespaces
+  - cgroups
+  - enablement
+  - exfiltrate
+  - distro
+  - Overlayfs
+  - hostname
+  - devpts
+  - ptys
+  - overlayfs
+  - ns
+  - upperdirs
+  - securebits
+  - dirs
+  - syscalls
+  - syscall
+  - tracee
+  - ptrace
+  - netns
+  - slirp
+  - nftables
+  - Cgroups
+  - subtree
+  - chowning
+  - pid
+  - Ptrace
+  - Podman