fix: New README, new documentation for developpers, and many install.sh and update.sh fixes

README.md

@@ -1,52 +1,99 @@
-# Atlas Desktop installer
+# Atlas Desktop
 
-This project is an automated installer for the Atlas Desktop.
+A fully automated Archlinux setup for people that care about their computer.
 
-## Disclaimer
+```sh
+curl -fsSL https://forge.oblic-parallels.fr/guillm/atlas-desktop/raw/branch/main/scripts/install.sh | bash
+```
 
-### ⚠ Use at your own risk.
 
-Some platforms may not yet be supported such as Nvidia graphic cards for which you'll have to install all the drivers yourself. Sadly I don't have any equipment to test that out.
+## What's included
  
-Also you will very probably miss some software you're used to. I'll strongly recommend you to check the [Additionnal packages](https://hedgedoc.oblic-parallels.fr/s/JSR33pjd_#Additional-packages) section to know about some open source utilities that fit perfectly within the desktop. 
+- **Window manager**: Hyprland
-More generally give a look to the [Quick start guide](https://hedgedoc.oblic-parallels.fr/s/JSR33pjd_)
+- **Status bar**: Waybar
-
+- **Display manager**: Ly
-If something doesn't work or behaves anormally don't hesitate to contact me so that it will be fixed for future users.
+- **Launcher**: Rofi
+- **Notifications center**: Swaync
+- **Terminal**: Foot
+- **Shell**: Zsh + Zinit + Powerlevel10k
 
 
 ## Requirements
 
-You'll just need an already functional (even basic) **Arch Linux** system with `sudo` installed.
+- A basic Arch Linux install (cli is enough, no DE required)
-Setup will take care of configuring AppArmor and Zram if it hasn't been done yet.
+- A user account with `sudo` access
+- `git` installed (`sudo pacman -Sy git`)
+- Internet connection
+
+Setup will take care of configuring AppArmor and Zram or even firewall if you haven't done it yet.
+
+## Installation
+
+**Disclaimer**: Some platforms may not yet be supported such as Nvidia graphic cards for which you'll have to install all the drivers yourself. Sadly I don't have any equipment to test that out.
 
 
-## Usage
+```sh
-
+curl -fsSL https://forge.oblic-parallels.fr/guillm/atlas-desktop/raw/branch/main/scripts/install.sh | bash
-Very simple, clone the project (or download it directly from the web interface)
-```sh=
-git clone https://forge.oblic-parallels.fr/guillm/atlas-install
 ```
-And run `setup.sh`
-```sh=
-./setup.sh
-```
-
 Then just follow the instructions and you should be good to go !
-If you encounter any error or bug, don't hesitate to open an issue on this repo.
+After the setup finishes you may need to reboot in order to login:
+```sh
+sudo reboot
+```
+
+> **Note**: If you encounter any error or bug, don't hesitate to open an issue on this repo.
+ 
+> **Note:** After installation the original clone is no longer needed.
+> `~/.dotfiles` is the real repo and is what the updater tracks.
+
 
 ## Configuration
 
-I suggest you to give a look to the packages that will be installed on your system as it's important to know how things will work or to disable some things you wouldn't necessarely want.
+I suggest you to give a look to the [Quick start guide](https://hedgedoc.oblic-parallels.fr/s/JSR33pjd_) that explains how the system works if you're not used to it.
-I particularly think of helix which is used as the default text editor but may not suit some people needs.
+As you will very probably miss some software you're used to. I'll strongly recommend you to check the [Additionnal packages](https://hedgedoc.oblic-parallels.fr/s/JSR33pjd_#Additional-packages) section to know about some open source utilities that fit perfectly within the desktop. 
 
 Note that the default keyboard layout is QWERTY (us-fr). You can switch with the AZERTY layout by using `Mod+Ctrl+Space`. That said, the default layout already has french accents if you need them.
 If you need to modify the layout, go to `~/.config/hypr/config/default/kb_layouts`.
 
-### Defaults
 
-I'm working on a system to easily change the default programs. I don't know yet if it will result into anything but it's worth trying.
+## Staying up to date
+
+```sh
+atlas-update
+```
+
+This will:
+
+- Fetch origin/main and show new commits
+- Detect conflicts between upstream changes and local edits, asking you which to keep per file
+- Pull and re-stow config/
+- Re-prompt for any new optional groups added upstream
+
+
+## Troubleshooting
+ 
+**Stow reports conflicts on first install**
+- Existing real files that clash with stow links are automatically renamed to `<file>.bak`.
+ 
+**An AUR package failed to install**
+- The installer reports it and continues. It won't be saved to state, so `atlas-update` will retry it next run.
+ 
+**`atlas-update` says "already up to date" but a package is missing**
+- Delete its state file to force a re-sync:
+```bash
+rm ~/.atlas-dotfiles/.state/packages/mygroup.pkgs
+atlas-update
+```
+ 
+**Waybar doesn't reload after switching layout**
+- Reload desktop using `Mod+Shift+R` or run the following command:
+```bash
+pkill waybar && waybar &
+```
+
 
 ## Future improvements
 
+- Waybar switch script
+- A defaults system allowing you to easily choose your default programs
 - Nvidia cards handling
-- Cleaner way to enable/disable some packages / configuratuions

doc/Developpers.md

@@ -0,0 +1,57 @@
+# Developpers documentation
+
+## Repository structure
+ 
+```
+dotfiles/
+├── install.sh
+├── scripts/
+│   └── update.sh               ← dotfiles-update
+├── packages/
+│   ├── core.pkgs               ← always installed
+│   ├── desktop.pkgs            ← always installed (automatic)
+│   ├── aur.pkgs                ← AUR packages (paru)
+│   ├── intel-cpu.pkgs          ← auto: Intel CPU
+│   ├── amd-cpu.pkgs            ← auto: AMD CPU
+│   ├── intel-gpu.pkgs          ← auto: Intel GPU
+│   ├── amd-gpu.pkgs            ← auto: AMD GPU
+│   ├── nvidia.pkgs             ← auto: NVIDIA GPU
+│   ├── gaming.pkgs             ← optional
+│   ├── development.pkgs        ← optional
+│   ├── ...
+│   ├── optional.groups         ← lists which groups are optional
+│   └── <group>.desc            ← one-line description shown in installer
+└── config/                     ← stow package; mirrors $HOME
+    ├── .config/
+    │   ├── hypr/
+    │   ├── waybar/
+    │   │   ├── vertical/
+    │   │   └── horizontal/
+    │   ├── rofi/
+    │   └── ...
+    └── .local/
+        └── bin/
+            └── atlas-update
+```
+ 
+### Package group conventions
+ 
+| File | When installed |
+|---|---|
+| `core.pkgs` | Always |
+| Any unlisted `*.pkgs` (e.g. `desktop.pkgs`) | Always (automatic) |
+| `aur.pkgs` | Always, via paru |
+| `intel-gpu.pkgs`, `amd-gpu.pkgs`, etc. | Auto-detected via `lspci` / `/proc/cpuinfo` |
+| Groups listed in `optional.groups` | User-chosen during install, remembered on updates |
+ 
+To add a new automatic group: create `packages/mygroup.pkgs` and commit.
+To add a new optional group: also add its name to `packages/optional.groups` and optionally a `packages/mygroup.desc` one-liner.
+ 
+
+## Package state tracking
+ 
+After each install or update, a snapshot of every installed group is saved to `~/.dotfiles/.state/packages/<group>`. On the next run, each group is diffed:
+ 
+- **New packages** in the `.pkgs` file → installed automatically
+- **Removed packages** → you are asked before uninstalling
+Delete `~/.dotfiles/.state/` to reset all state and force a full reinstall on the next update.

scripts/install.sh

@@ -497,6 +497,9 @@ install_packages() {
   local pkg_file pkgs group
 
   # Helper: install a group and save state
+  # Note: AUR packages are installed one-by-one so a single failure does not abort
+  # the whole group. Official repo packages are bulk-installed with a per-
+  # package fallback. Only successfully installed packages are saved to state.
   install_group() {
     local group="$1"
     local pkg_file="$PACKAGES_DIR/${group}.pkgs"
@@ -506,25 +509,114 @@ install_packages() {
     (( ${#pkgs[@]} == 0 )) && { info "${group}: empty — skipping"; return; }
 
     step "Group: ${group} (${#pkgs[@]} packages)"
+
+    local succeeded=() failed=()
+
     if [[ $group == aur ]]; then
-      run_quiet "  Installing ${group}" paru_install "${pkgs[@]}"
+      for pkg in "${pkgs[@]}"; do
+        local tmp; tmp=$(mktemp)
+        if [[ $IS_TTY == true ]]; then
+          spinner_start "  [aur] $pkg"
+          if paru -S --needed --noconfirm "$pkg" >"$tmp" 2>&1; then
+            spinner_stop ok "[aur] $pkg"; succeeded+=("$pkg")
+          else
+            spinner_stop fail "[aur] $pkg"
+            warn "paru output:"; cat "$tmp" | indent; failed+=("$pkg")
+          fi
+        else
+          printf "  ...  [aur] %s\n" "$pkg"
+          if paru -S --needed --noconfirm "$pkg" >"$tmp" 2>&1; then
+            ok "[aur] $pkg"; succeeded+=("$pkg")
+          else
+            err "[aur] $pkg"
+            warn "paru output:"; cat "$tmp" | indent; failed+=("$pkg")
+          fi
+        fi
+        rm -f "$tmp"
+      done
     else
       run_quiet "  Installing ${group}" pacman_install "${pkgs[@]}"
+      local tmp; tmp=$(mktemp)
+      if pacman_install "${pkgs[@]}" >"$tmp" 2>&1; then
+        succeeded=("${pkgs[@]}"); rm -f "$tmp"
+      else
+        rm -f "$tmp"
+        warn "Bulk install failed for group '${group}' — retrying per package"
+        for pkg in "${pkgs[@]}"; do
+          local tmp2; tmp2=$(mktemp)
+          if [[ $IS_TTY == true ]]; then
+            spinner_start "  [${group}] $pkg"
+            if pacman_install "$pkg" >"$tmp2" 2>&1; then
+              spinner_stop ok "[${group}] $pkg"; succeeded+=("$pkg")
+            else
+              spinner_stop fail "[${group}] $pkg"
+              warn "pacman output:"; cat "$tmp2" | indent; failed+=("$pkg")
+            fi
+          else
+            printf "  ...  [%s] %s\n" "$group" "$pkg"
+            if pacman_install "$pkg" >"$tmp2" 2>&1; then
+              ok "[${group}] $pkg"; succeeded+=("$pkg")
+            else
+              err "[${group}] $pkg"
+              warn "pacman output:"; cat "$tmp2" | indent; failed+=("$pkg")
+            fi
+          fi
+          rm -f "$tmp2"
+        done
+      fi
     fi
-    save_pkg_list "$group" "${pkgs[@]}"
+
+    if (( ${#succeeded[@]} )); then
+      save_pkg_list "$group" "${succeeded[@]}"
+    fi
+
+    if (( ${#failed[@]} )); then
+      warn "Failed in group '${group}' (will retry on next update):"
+      for pkg in "${failed[@]}"; do
+        printf "       - %s\n" "$pkg"
+      done
+    fi
+    return 0
   }
 
   # stow itself (needed for the next step)
   run_quiet "Ensuring stow is present" sudo pacman -S --needed --noconfirm stow
 
-  # Core
+  # Build the set of groups that are handled specially so we can exclude them
+  # when iterating all .pkgs files for automatic groups.
+  local hw_groups=("${HW_CPU}-cpu" "${HW_GPU}-gpu")
+  local optional_group_names=()
+  local optional_file="$PACKAGES_DIR/optional.groups"
+  if [[ -f $optional_file ]]; then
+    mapfile -t optional_group_names < <(grep -v '^\s*#' "$optional_file" | grep -v '^\s*$')
+  fi
+
+  is_special_group() {
+    local g="$1"
+    # Returns 0 if the group is hw, optional, aur, or security (handled separately)
+    [[ $g == aur || $g == security ]] && return 0
+    for hw in "${hw_groups[@]}"; do [[ $g == "$hw" ]] && return 0; done
+    for og in "${optional_group_names[@]}"; do [[ $g == "$og" ]] && return 0; done
+    return 1
+  }
+
+  # 1. Core
   install_group "core"
 
-  # Hardware
+  # 2. Hardware (auto-detected)
-  install_group "${HW_CPU}-cpu" 2>/dev/null || true
+  install_group "${HW_CPU}-cpu"
-  install_group "${HW_GPU}-gpu" 2>/dev/null || true
+  install_group "${HW_GPU}-gpu"
 
-  # Security extras
+  # 3. All remaining automatic groups (every .pkgs file that is not special)
+  while IFS= read -r pkg_file; do
+    local group; group=$(basename "$pkg_file" .pkgs)
+    is_special_group "$group" && continue
+    [[ $group == core ]] && continue   # already done above
+    install_group "$group"
+  done < <(find "$PACKAGES_DIR" -maxdepth 1 -name "*.pkgs" | sort)
+
+
+  # 4. Security extras
   if [[ $INSTALL_SECURITY == true ]]; then
     local sec_pkgs=(ufw apparmor zram-generator)
     step "Security extras"
@@ -532,12 +624,12 @@ install_packages() {
     save_pkg_list "security" "${sec_pkgs[@]}"
   fi
 
-  # Optional chosen groups
+  # 5. Optional chosen groups
   for group in "${CHOSEN_OPTIONAL_GROUPS[@]}"; do
     install_group "$group"
   done
 
-  # AUR group (always, if paru is present)
+  # 6. AUR group
   install_group "aur"
 
   phase_done
@@ -547,9 +639,9 @@ install_packages() {
 #  STEP 9 — Clone into ~/.atlas-dotfiles and stow
 # ─────────────────────────────────────────────────────────────────────────────
 stow_dotfiles() {
-  phase "Copying and stowing dotfiles"
+  phase "Cloning and stowing dotfiles"
 
-  # ~/.atlas-dotfiles is the permanent home of the repo. They can delete the original
+  # ~/.atlas-dotfiles is the permanent home of the repo. You can delete the original
   # clone after installation without breaking anything.
   local remote_url
   remote_url=$(git -C "$REPO_DIR" remote get-url origin 2>/dev/null || true)

scripts/update.sh

@@ -15,6 +15,8 @@ STATE_DIR="$DOTFILES_DIR/.state"
 PKG_STATE_DIR="$STATE_DIR/packages"
 STATE_FILE="$STATE_DIR/update.state"
 PACKAGES_DIR="$DOTFILES_DIR/packages"
+STOW_DIR="$DOTFILES_DIR"
+STOW_PKG="config"
 STOW_TARGET="$HOME"
 
 # ── Colours ──────────────────────────────────────────────────────────────────
@@ -188,20 +190,32 @@ git_fetch_and_check() {
   OLD_HASH="$local_hash"
 }
 
-# ── Conflict detection ────────────────────────────────────────────────────────
+# ── Change detection ────────────────────────────────────────────────────────────────
-collect_changed_files() {
+
-  # Files changed inside the config/ stow package between old and new commit.
+# Files changed inside config/ (stow package) — used for conflict detection.
-  # Strip the leading "config/" prefix so paths are relative to $HOME,
+# Paths are stripped of the "config/" prefix so they match $HOME-relative targets.
-  # matching what stow creates as symlink targets.
+collect_changed_config_files() {
   git -C "$DOTFILES_DIR" diff --name-only "${OLD_HASH}" "${NEW_HASH}" \
     | grep '^config/' \
     | sed 's|^config/||' \
     || true
 }
 
+# Returns 0 (true) if any file under packages/ changed between the two commits.
+packages_changed() {
+  git -C "$DOTFILES_DIR" diff --name-only "${OLD_HASH}" "${NEW_HASH}" \
+    | grep -q '^packages/'
+}
+
+# Returns 0 (true) if any file under scripts/ changed between the two commits.
+scripts_changed() {
+  git -C "$DOTFILES_DIR" diff --name-only "${OLD_HASH}" "${NEW_HASH}" \
+    | grep -q '^scripts/'
+}
+
 handle_conflicts() {
   local repo_changed_files
-  mapfile -t repo_changed_files < <(collect_changed_files)
+  mapfile -t repo_changed_files < <(collect_changed_config_files)
 
   if (( ${#repo_changed_files[@]} == 0 )); then
     return
@@ -502,10 +516,37 @@ main() {
   if [[ $HAS_UPDATE == true ]]; then
     handle_conflicts
     apply_git_update
+
+    # Re-stow config/ whenever dotfiles changed
     apply_stow
+
+    # Re-stow scripts/ when it changed (keeps ~/.local/bin helpers up to date)
+    if scripts_changed; then
+      info "scripts/ changed — re-linking binaries"
+      local err_file; err_file=$(mktemp)
+      if stow --dir="$DOTFILES_DIR" --target="$HOME" --restow scripts \
+           2>"$err_file"; then
+        ok "stow: scripts"
+      else
+        warn "stow: scripts (errors below)"
+        while IFS= read -r line; do
+          echo "       ${DIM}${line}${RESET}"
+        done < "$err_file"
+      fi
+      rm -f "$err_file"
+    fi
+
     state_set "last_commit" "$NEW_HASH"
+
+    # Re-process packages whenever packages/ changed, even if no git update
+    # produced new dotfiles — package lists are independent of stowed files.
+    if packages_changed; then
+      info "packages/ changed — running full package sync"
+    fi
   fi
 
+  # Package sync runs on every invocation (diff vs saved state catches changes).
+  # This also handles the case where a previous run partially failed.
   process_packages
   process_aur_group