Update scripts to keep SOUL.md idempotent. Add release upgrade framework.

README.md

@@ -30,6 +30,7 @@ The installer will:
 - Add `~/.config/mosaic/bin` to your PATH
 - Sync runtime adapters and skills
 - Run a health audit
+- Detect existing installs and prompt to keep or overwrite local files
 - Prompt you to run `mosaic init` to set up your agent identity
 
 ## First Run
@@ -96,24 +97,58 @@ mosaic init                # Generate SOUL.md (agent identity)
 mosaic doctor              # Health audit — detect drift and missing files
 mosaic sync                # Sync skills from canonical source
 mosaic bootstrap <path>    # Bootstrap a repo with Mosaic standards
-mosaic upgrade [path]      # Clean up stale per-project files (see below)
+mosaic upgrade check       # Check release upgrade status (no changes)
-mosaic upgrade --all       # Upgrade all projects in ~/src
+mosaic upgrade             # Upgrade installed Mosaic release (keeps SOUL.md by default)
-mosaic upgrade --dry-run   # Preview without changes
+mosaic upgrade --dry-run   # Preview release upgrade without changes
+mosaic upgrade --ref main  # Upgrade from a specific branch/tag/commit ref
+mosaic upgrade --overwrite # Upgrade release and overwrite local files
+mosaic upgrade project ... # Project file cleanup mode (see below)
 ```
 
+## Upgrading Mosaic Release
+
+Upgrade the installed framework in place:
+
+```bash
+# Default (safe): keep local SOUL.md + memory
+mosaic upgrade
+
+# Check current/target release info without changing files
+mosaic upgrade check
+
+# Non-interactive
+mosaic upgrade --yes
+
+# Pull a specific ref
+mosaic upgrade --ref main
+
+# Force full overwrite (fresh install semantics)
+mosaic upgrade --overwrite --yes
+```
+
+`mosaic upgrade` re-runs the remote installer and passes install mode controls (`keep`/`overwrite`).
+This is the manual upgrade path today and is suitable for future app-driven update checks.
+
 ## Upgrading Projects
 
 After centralizing AGENTS.md and SOUL.md, existing projects may have stale files:
 
 ```bash
 # Preview what would change across all projects
-mosaic upgrade --all --dry-run
+mosaic upgrade project --all --dry-run
 
 # Apply to all projects
-mosaic upgrade --all
+mosaic upgrade project --all
 
 # Apply to a specific project
-mosaic upgrade ~/src/my-project
+mosaic upgrade project ~/src/my-project
+```
+
+Backward compatibility is preserved for historical usage:
+
+```bash
+mosaic upgrade --all          # still routes to project-upgrade
+mosaic upgrade ~/src/my-repo  # still routes to project-upgrade
 ```
 
 What it does per project:
@@ -186,6 +221,10 @@ Pull the latest and re-run the installer:
 cd ~/src/mosaic-bootstrap && git pull && bash install.sh
 ```
 
+If an existing install is detected, the installer prompts for:
+- `keep` (recommended): preserve local `SOUL.md` and `memory/`
+- `overwrite`: replace everything in `~/.config/mosaic`
+
 Or use the one-liner again — it always pulls the latest:
 
 ```bash

bin/mosaic

@@ -14,6 +14,9 @@ set -euo pipefail
 #   mosaic doctor [args...]       Health audit
 #   mosaic sync [args...]         Sync skills
 #   mosaic bootstrap <path>       Bootstrap a repo
+#   mosaic upgrade release         Upgrade installed Mosaic release
+#   mosaic upgrade check           Check release upgrade status (no changes)
+#   mosaic upgrade project [args]  Upgrade project-local stale files
 
 MOSAIC_HOME="${MOSAIC_HOME:-$HOME/.config/mosaic}"
 VERSION="0.1.0"
@@ -34,7 +37,10 @@ Management:
   doctor [args...]       Audit runtime state and detect drift
   sync [args...]         Sync skills from canonical source
   bootstrap <path>       Bootstrap a repo with Mosaic standards
-  upgrade [path]         Clean up stale SOUL.md/CLAUDE.md in a project
+  upgrade [mode] [args]  Upgrade release (default) or project files
+  upgrade check          Check release upgrade status (no changes)
+  release-upgrade [...]  Upgrade installed Mosaic release
+  project-upgrade [...]  Clean up stale SOUL.md/CLAUDE.md in a project
 
 Options:
   -h, --help             Show this help
@@ -147,11 +153,54 @@ run_bootstrap() {
   exec "$MOSAIC_HOME/bin/mosaic-bootstrap-repo" "$@"
 }
 
-run_upgrade() {
+run_release_upgrade() {
+  check_mosaic_home
+  exec "$MOSAIC_HOME/bin/mosaic-release-upgrade" "$@"
+}
+
+run_project_upgrade() {
   check_mosaic_home
   exec "$MOSAIC_HOME/bin/mosaic-upgrade" "$@"
 }
 
+run_upgrade() {
+  check_mosaic_home
+
+  # Default: upgrade installed release
+  if [[ $# -eq 0 ]]; then
+    run_release_upgrade
+  fi
+
+  case "$1" in
+    release)
+      shift
+      run_release_upgrade "$@"
+      ;;
+    check)
+      shift
+      run_release_upgrade --dry-run "$@"
+      ;;
+    project)
+      shift
+      run_project_upgrade "$@"
+      ;;
+
+    # Backward compatibility for historical project-upgrade usage.
+    --all|--root)
+      run_project_upgrade "$@"
+      ;;
+    --dry-run|--ref|--keep|--overwrite|-y|--yes)
+      run_release_upgrade "$@"
+      ;;
+    -*)
+      run_release_upgrade "$@"
+      ;;
+    *)
+      run_project_upgrade "$@"
+      ;;
+  esac
+}
+
 # Main router
 if [[ $# -eq 0 ]]; then
   usage
@@ -170,6 +219,8 @@ case "$command" in
   sync)       run_sync "$@" ;;
   bootstrap)  run_bootstrap "$@" ;;
   upgrade)    run_upgrade "$@" ;;
+  release-upgrade) run_release_upgrade "$@" ;;
+  project-upgrade) run_project_upgrade "$@" ;;
   help|-h|--help)  usage ;;
   version|-v|--version) echo "mosaic $VERSION" ;;
   *)

bin/mosaic-release-upgrade

@@ -0,0 +1,124 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# mosaic-release-upgrade — Upgrade installed Mosaic framework release.
+#
+# This re-runs the remote installer with explicit install mode controls.
+# Default behavior is safe/idempotent (keep SOUL.md + memory).
+#
+# Usage:
+#   mosaic-release-upgrade
+#   mosaic-release-upgrade --ref main --keep
+#   mosaic-release-upgrade --ref v0.2.0 --overwrite --yes
+
+MOSAIC_HOME="${MOSAIC_HOME:-$HOME/.config/mosaic}"
+REMOTE_SCRIPT_URL="${MOSAIC_REMOTE_INSTALL_URL:-https://git.mosaicstack.dev/mosaic/bootstrap/raw/branch/main/remote-install.sh}"
+BOOTSTRAP_REF="${MOSAIC_BOOTSTRAP_REF:-main}"
+INSTALL_MODE="${MOSAIC_INSTALL_MODE:-keep}" # keep|overwrite
+YES=false
+DRY_RUN=false
+
+usage() {
+  cat <<USAGE
+Usage: $(basename "$0") [options]
+
+Upgrade the installed Mosaic framework release.
+
+Options:
+  --ref <name>         Bootstrap archive ref (branch/tag/commit). Default: main
+  --keep               Keep local files (SOUL.md, memory/) during upgrade (default)
+  --overwrite          Overwrite target install directory contents
+  -y, --yes            Skip confirmation prompt
+  --dry-run            Show actions without executing
+  -h, --help           Show this help
+USAGE
+}
+
+while [[ $# -gt 0 ]]; do
+  case "$1" in
+    --ref)
+      [[ $# -lt 2 ]] && { echo "Missing value for --ref" >&2; exit 1; }
+      BOOTSTRAP_REF="$2"
+      shift 2
+      ;;
+    --keep)
+      INSTALL_MODE="keep"
+      shift
+      ;;
+    --overwrite)
+      INSTALL_MODE="overwrite"
+      shift
+      ;;
+    -y|--yes)
+      YES=true
+      shift
+      ;;
+    --dry-run)
+      DRY_RUN=true
+      shift
+      ;;
+    -h|--help)
+      usage
+      exit 0
+      ;;
+    *)
+      echo "Unknown argument: $1" >&2
+      usage >&2
+      exit 1
+      ;;
+  esac
+done
+
+case "$INSTALL_MODE" in
+  keep|overwrite) ;;
+  *)
+    echo "[mosaic-release-upgrade] Invalid install mode: $INSTALL_MODE" >&2
+    exit 1
+    ;;
+esac
+
+current_version="unknown"
+if [[ -x "$MOSAIC_HOME/bin/mosaic" ]]; then
+  current_version="$("$MOSAIC_HOME/bin/mosaic" --version 2>/dev/null | awk '{print $2}' || true)"
+  [[ -n "$current_version" ]] || current_version="unknown"
+fi
+
+echo "[mosaic-release-upgrade] Current version: $current_version"
+echo "[mosaic-release-upgrade] Target ref: $BOOTSTRAP_REF"
+echo "[mosaic-release-upgrade] Install mode: $INSTALL_MODE"
+echo "[mosaic-release-upgrade] Installer URL: $REMOTE_SCRIPT_URL"
+
+if [[ "$DRY_RUN" == "true" ]]; then
+  echo "[mosaic-release-upgrade] Dry run: no changes applied."
+  exit 0
+fi
+
+if [[ "$YES" != "true" && -t 0 ]]; then
+  printf "Proceed with Mosaic release upgrade? [y/N]: "
+  read -r confirm
+  case "${confirm:-n}" in
+    y|Y|yes|YES) ;;
+    *)
+      echo "[mosaic-release-upgrade] Aborted."
+      exit 1
+      ;;
+  esac
+fi
+
+if command -v curl >/dev/null 2>&1; then
+  curl -sL "$REMOTE_SCRIPT_URL" | \
+    MOSAIC_BOOTSTRAP_REF="$BOOTSTRAP_REF" \
+    MOSAIC_INSTALL_MODE="$INSTALL_MODE" \
+    MOSAIC_HOME="$MOSAIC_HOME" \
+    sh
+elif command -v wget >/dev/null 2>&1; then
+  wget -qO- "$REMOTE_SCRIPT_URL" | \
+    MOSAIC_BOOTSTRAP_REF="$BOOTSTRAP_REF" \
+    MOSAIC_INSTALL_MODE="$INSTALL_MODE" \
+    MOSAIC_HOME="$MOSAIC_HOME" \
+    sh
+else
+  echo "[mosaic-release-upgrade] ERROR: curl or wget required." >&2
+  exit 1
+fi
+

bin/mosaic-release-upgrade.ps1

@@ -0,0 +1,65 @@
+# mosaic-release-upgrade.ps1 — Upgrade installed Mosaic framework release (Windows)
+#
+# Usage:
+#   mosaic-release-upgrade.ps1
+#   mosaic-release-upgrade.ps1 -Ref main -Keep
+#   mosaic-release-upgrade.ps1 -Ref v0.2.0 -Overwrite -Yes
+#
+param(
+    [string]$Ref = $(if ($env:MOSAIC_BOOTSTRAP_REF) { $env:MOSAIC_BOOTSTRAP_REF } else { "main" }),
+    [switch]$Keep,
+    [switch]$Overwrite,
+    [switch]$Yes,
+    [switch]$DryRun
+)
+
+$ErrorActionPreference = "Stop"
+
+$MosaicHome = if ($env:MOSAIC_HOME) { $env:MOSAIC_HOME } else { Join-Path $env:USERPROFILE ".config\mosaic" }
+$RemoteInstallerUrl = if ($env:MOSAIC_REMOTE_INSTALL_URL) {
+    $env:MOSAIC_REMOTE_INSTALL_URL
+} else {
+    "https://git.mosaicstack.dev/mosaic/bootstrap/raw/branch/main/remote-install.ps1"
+}
+
+$installMode = if ($Overwrite) { "overwrite" } elseif ($Keep) { "keep" } elseif ($env:MOSAIC_INSTALL_MODE) { $env:MOSAIC_INSTALL_MODE } else { "keep" }
+if ($installMode -notin @("keep", "overwrite")) {
+    Write-Host "[mosaic-release-upgrade] Invalid install mode: $installMode" -ForegroundColor Red
+    exit 1
+}
+
+$currentVersion = "unknown"
+$mosaicCmd = Join-Path $MosaicHome "bin\mosaic.ps1"
+if (Test-Path $mosaicCmd) {
+    try {
+        $currentVersion = (& $mosaicCmd --version) -replace '^mosaic\s+', ''
+    }
+    catch {
+        $currentVersion = "unknown"
+    }
+}
+
+Write-Host "[mosaic-release-upgrade] Current version: $currentVersion"
+Write-Host "[mosaic-release-upgrade] Target ref: $Ref"
+Write-Host "[mosaic-release-upgrade] Install mode: $installMode"
+Write-Host "[mosaic-release-upgrade] Installer URL: $RemoteInstallerUrl"
+
+if ($DryRun) {
+    Write-Host "[mosaic-release-upgrade] Dry run: no changes applied."
+    exit 0
+}
+
+if (-not $Yes) {
+    $confirmation = Read-Host "Proceed with Mosaic release upgrade? [y/N]"
+    if ($confirmation -notin @("y", "Y", "yes", "YES")) {
+        Write-Host "[mosaic-release-upgrade] Aborted."
+        exit 1
+    }
+}
+
+$env:MOSAIC_BOOTSTRAP_REF = $Ref
+$env:MOSAIC_INSTALL_MODE = $installMode
+$env:MOSAIC_HOME = $MosaicHome
+
+Invoke-RestMethod -Uri $RemoteInstallerUrl | Invoke-Expression
+

bin/mosaic.ps1

@@ -31,7 +31,10 @@ Management:
   doctor [args...]       Audit runtime state and detect drift
   sync [args...]         Sync skills from canonical source
   bootstrap <path>       Bootstrap a repo with Mosaic standards
-  upgrade [path]         Clean up stale SOUL.md/CLAUDE.md in a project
+  upgrade [mode] [args]  Upgrade release (default) or project files
+  upgrade check          Check release upgrade status (no changes)
+  release-upgrade [...]  Upgrade installed Mosaic release
+  project-upgrade [...]  Clean up stale SOUL.md/CLAUDE.md in a project
 
 Options:
   -h, --help             Show this help
@@ -142,6 +145,48 @@ switch ($command) {
         & (Join-Path $MosaicHome "bin\mosaic-bootstrap-repo") @remaining
     }
     "upgrade" {
+        Assert-MosaicHome
+        if ($remaining.Count -eq 0) {
+            & (Join-Path $MosaicHome "bin\mosaic-release-upgrade.ps1")
+            break
+        }
+
+        $mode = $remaining[0]
+        $tail = if ($remaining.Count -gt 1) { $remaining[1..($remaining.Count - 1)] } else { @() }
+
+        switch -Regex ($mode) {
+            "^release$" {
+                & (Join-Path $MosaicHome "bin\mosaic-release-upgrade.ps1") @tail
+            }
+            "^check$" {
+                & (Join-Path $MosaicHome "bin\mosaic-release-upgrade.ps1") -DryRun @tail
+            }
+            "^project$" {
+                Write-Host "[mosaic] NOTE: mosaic-upgrade requires bash. Use Git Bash or WSL." -ForegroundColor Yellow
+                & (Join-Path $MosaicHome "bin\mosaic-upgrade") @tail
+            }
+            "^(--all|--root)$" {
+                Write-Host "[mosaic] NOTE: mosaic-upgrade requires bash. Use Git Bash or WSL." -ForegroundColor Yellow
+                & (Join-Path $MosaicHome "bin\mosaic-upgrade") @remaining
+            }
+            "^(--dry-run|--ref|--keep|--overwrite|-y|--yes)$" {
+                & (Join-Path $MosaicHome "bin\mosaic-release-upgrade.ps1") @remaining
+            }
+            "^-.*" {
+                & (Join-Path $MosaicHome "bin\mosaic-release-upgrade.ps1") @remaining
+            }
+            default {
+                Write-Host "[mosaic] NOTE: treating positional argument as project path." -ForegroundColor Yellow
+                Write-Host "[mosaic] NOTE: mosaic-upgrade requires bash. Use Git Bash or WSL." -ForegroundColor Yellow
+                & (Join-Path $MosaicHome "bin\mosaic-upgrade") @remaining
+            }
+        }
+    }
+    "release-upgrade" {
+        Assert-MosaicHome
+        & (Join-Path $MosaicHome "bin\mosaic-release-upgrade.ps1") @remaining
+    }
+    "project-upgrade" {
         Assert-MosaicHome
         Write-Host "[mosaic] NOTE: mosaic-upgrade requires bash. Use Git Bash or WSL." -ForegroundColor Yellow
         & (Join-Path $MosaicHome "bin\mosaic-upgrade") @remaining

install.ps1

@@ -8,16 +8,96 @@ $ErrorActionPreference = "Stop"
 
 $SourceDir = $PSScriptRoot
 $TargetDir = if ($env:MOSAIC_HOME) { $env:MOSAIC_HOME } else { Join-Path $env:USERPROFILE ".config\mosaic" }
+$InstallMode = if ($env:MOSAIC_INSTALL_MODE) { $env:MOSAIC_INSTALL_MODE.ToLowerInvariant() } else { "prompt" } # prompt|keep|overwrite
+$PreservePaths = @("SOUL.md", "memory")
 
 function Write-Ok   { param([string]$Msg) Write-Host "  ✓ " -ForegroundColor Green -NoNewline; Write-Host $Msg }
 function Write-Warn { param([string]$Msg) Write-Host "  ⚠ " -ForegroundColor Yellow -NoNewline; Write-Host $Msg }
 function Write-Fail { param([string]$Msg) Write-Host "  ✗ " -ForegroundColor Red -NoNewline; Write-Host $Msg }
 function Write-Step { param([string]$Msg) Write-Host ""; Write-Host $Msg -ForegroundColor White -BackgroundColor DarkGray }
 
+function Test-ExistingInstall {
+    if (-not (Test-Path $TargetDir)) { return $false }
+    return (Test-Path (Join-Path $TargetDir "bin\mosaic")) -or (Test-Path (Join-Path $TargetDir "AGENTS.md")) -or (Test-Path (Join-Path $TargetDir "SOUL.md"))
+}
+
+function Select-InstallMode {
+    switch ($InstallMode) {
+        "prompt" { }
+        "keep" { return }
+        "overwrite" { return }
+        default {
+            Write-Fail "Invalid MOSAIC_INSTALL_MODE '$InstallMode'. Use: prompt, keep, overwrite."
+            exit 1
+        }
+    }
+
+    if (-not (Test-ExistingInstall)) {
+        $script:InstallMode = "overwrite"
+        return
+    }
+
+    if (-not [Environment]::UserInteractive) {
+        Write-Warn "Existing install detected without interactive input; defaulting to keep local files."
+        $script:InstallMode = "keep"
+        return
+    }
+
+    Write-Host ""
+    Write-Host "Existing Mosaic install detected at: $TargetDir"
+    Write-Host "Choose reinstall mode:"
+    Write-Host "  1) keep      Keep local files (SOUL.md, memory/) while updating framework"
+    Write-Host "  2) overwrite Replace everything in $TargetDir"
+    Write-Host "  3) cancel    Abort install"
+    $selection = Read-Host "Selection [1/2/3] (default: 1)"
+
+    $normalizedSelection = if ($null -eq $selection) { "" } else { $selection.ToLowerInvariant() }
+    switch ($normalizedSelection) {
+        "" { $script:InstallMode = "keep" }
+        "1" { $script:InstallMode = "keep" }
+        "k" { $script:InstallMode = "keep" }
+        "keep" { $script:InstallMode = "keep" }
+        "2" { $script:InstallMode = "overwrite" }
+        "o" { $script:InstallMode = "overwrite" }
+        "overwrite" { $script:InstallMode = "overwrite" }
+        "3" { Write-Fail "Install cancelled."; exit 1 }
+        "c" { Write-Fail "Install cancelled."; exit 1 }
+        "cancel" { Write-Fail "Install cancelled."; exit 1 }
+        default {
+            Write-Warn "Unrecognized selection '$selection'; defaulting to keep."
+            $script:InstallMode = "keep"
+        }
+    }
+}
+
 # ── Install framework ────────────────────────────────────────
 Write-Step " Installing Mosaic framework "
 
 if (-not (Test-Path $TargetDir)) { New-Item -ItemType Directory -Path $TargetDir -Force | Out-Null }
+Select-InstallMode
+
+if ($InstallMode -eq "keep") {
+    Write-Ok "Install mode: keep local SOUL.md/memory while updating framework"
+}
+else {
+    Write-Ok "Install mode: overwrite existing files"
+}
+
+$preserveTmp = $null
+if ($InstallMode -eq "keep") {
+    $preserveTmp = Join-Path ([System.IO.Path]::GetTempPath()) ("mosaic-preserve-" + [Guid]::NewGuid().ToString("N"))
+    New-Item -ItemType Directory -Path $preserveTmp -Force | Out-Null
+    foreach ($relPath in $PreservePaths) {
+        $src = Join-Path $TargetDir $relPath
+        if (Test-Path $src) {
+            $dstParent = Join-Path $preserveTmp (Split-Path $relPath -Parent)
+            if (-not [string]::IsNullOrEmpty($dstParent) -and -not (Test-Path $dstParent)) {
+                New-Item -ItemType Directory -Path $dstParent -Force | Out-Null
+            }
+            Copy-Item $src (Join-Path $preserveTmp $relPath) -Recurse -Force
+        }
+    }
+}
 
 Get-ChildItem $TargetDir -Exclude ".git" | Remove-Item -Recurse -Force
 Get-ChildItem $SourceDir -Exclude ".git" | ForEach-Object {
@@ -30,6 +110,24 @@ Get-ChildItem $SourceDir -Exclude ".git" | ForEach-Object {
     }
 }
 
+if ($InstallMode -eq "keep" -and $null -ne $preserveTmp) {
+    foreach ($relPath in $PreservePaths) {
+        $src = Join-Path $preserveTmp $relPath
+        if (Test-Path $src) {
+            $dst = Join-Path $TargetDir $relPath
+            if (Test-Path $dst) {
+                Remove-Item $dst -Recurse -Force
+            }
+            $dstParent = Split-Path $dst -Parent
+            if (-not (Test-Path $dstParent)) {
+                New-Item -ItemType Directory -Path $dstParent -Force | Out-Null
+            }
+            Copy-Item $src $dst -Recurse -Force
+        }
+    }
+    Remove-Item -Path $preserveTmp -Recurse -Force -ErrorAction SilentlyContinue
+}
+
 Write-Ok "Framework installed to $TargetDir"
 
 # ── Post-install tasks ───────────────────────────────────────

install.sh

@@ -3,6 +3,8 @@ set -euo pipefail
 
 SOURCE_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 TARGET_DIR="${MOSAIC_HOME:-$HOME/.config/mosaic}"
+INSTALL_MODE="${MOSAIC_INSTALL_MODE:-prompt}" # prompt|keep|overwrite
+PRESERVE_PATHS=("SOUL.md" "memory")
 
 # Colors (disabled if not a terminal)
 if [[ -t 1 ]]; then
@@ -17,17 +19,125 @@ warn() { echo -e "  ${YELLOW}⚠${RESET} $1" >&2; }
 fail() { echo -e "  ${RED}✗${RESET} $1" >&2; }
 step() { echo -e "\n${BOLD}$1${RESET}"; }
 
+is_existing_install() {
+  [[ -d "$TARGET_DIR" ]] || return 1
+  [[ -f "$TARGET_DIR/bin/mosaic" || -f "$TARGET_DIR/AGENTS.md" || -f "$TARGET_DIR/SOUL.md" ]]
+}
+
+select_install_mode() {
+  case "$INSTALL_MODE" in
+    keep|overwrite|prompt) ;;
+    *)
+      fail "Invalid MOSAIC_INSTALL_MODE='$INSTALL_MODE'. Use: prompt, keep, overwrite."
+      exit 1
+      ;;
+  esac
+
+  if ! is_existing_install; then
+    INSTALL_MODE="overwrite"
+    return
+  fi
+
+  case "$INSTALL_MODE" in
+    keep|overwrite)
+      ;;
+    prompt)
+      if [[ -t 0 ]]; then
+        echo ""
+        echo "Existing Mosaic install detected at: $TARGET_DIR"
+        echo "Choose reinstall mode:"
+        echo "  1) keep      Keep local files (SOUL.md, memory/) while updating framework"
+        echo "  2) overwrite Replace everything in $TARGET_DIR"
+        echo "  3) cancel    Abort install"
+        printf "Selection [1/2/3] (default: 1): "
+        read -r selection
+
+        case "${selection:-1}" in
+          1|k|K|keep|KEEP) INSTALL_MODE="keep" ;;
+          2|o|O|overwrite|OVERWRITE) INSTALL_MODE="overwrite" ;;
+          3|c|C|cancel|CANCEL|n|N|no|NO)
+            fail "Install cancelled."
+            exit 1
+            ;;
+          *)
+            warn "Unrecognized selection '$selection'; defaulting to keep."
+            INSTALL_MODE="keep"
+            ;;
+        esac
+      else
+        warn "Existing install detected without interactive input; defaulting to keep local files."
+        INSTALL_MODE="keep"
+      fi
+      ;;
+  esac
+}
+
+sync_framework() {
+  local source_real target_real
+  source_real="$(cd "$SOURCE_DIR" && pwd -P)"
+  target_real="$(mkdir -p "$TARGET_DIR" && cd "$TARGET_DIR" && pwd -P)"
+
+  if [[ "$source_real" == "$target_real" ]]; then
+    warn "Source and target are the same directory; skipping file sync."
+    return
+  fi
+
+  if command -v rsync >/dev/null 2>&1; then
+    local rsync_args=(-a --delete --exclude ".git")
+
+    if [[ "$INSTALL_MODE" == "keep" ]]; then
+      local path
+      for path in "${PRESERVE_PATHS[@]}"; do
+        rsync_args+=(--exclude "$path")
+      done
+    fi
+
+    rsync "${rsync_args[@]}" "$SOURCE_DIR/" "$TARGET_DIR/"
+    return
+  fi
+
+  local preserve_tmp=""
+  if [[ "$INSTALL_MODE" == "keep" ]]; then
+    preserve_tmp="$(mktemp -d "${TMPDIR:-/tmp}/mosaic-preserve-XXXXXX")"
+    local path
+    for path in "${PRESERVE_PATHS[@]}"; do
+      if [[ -e "$TARGET_DIR/$path" ]]; then
+        mkdir -p "$preserve_tmp/$(dirname "$path")"
+        cp -R "$TARGET_DIR/$path" "$preserve_tmp/$path"
+      fi
+    done
+  fi
+
+  find "$TARGET_DIR" -mindepth 1 -maxdepth 1 ! -name ".git" -exec rm -rf {} +
+  cp -R "$SOURCE_DIR"/. "$TARGET_DIR"/
+  rm -rf "$TARGET_DIR/.git"
+
+  if [[ -n "$preserve_tmp" ]]; then
+    local path
+    for path in "${PRESERVE_PATHS[@]}"; do
+      if [[ -e "$preserve_tmp/$path" ]]; then
+        rm -rf "$TARGET_DIR/$path"
+        mkdir -p "$TARGET_DIR/$(dirname "$path")"
+        cp -R "$preserve_tmp/$path" "$TARGET_DIR/$path"
+      fi
+    done
+    rm -rf "$preserve_tmp"
+  fi
+}
+
 step "Installing Mosaic framework"
 
 mkdir -p "$TARGET_DIR"
+select_install_mode
 
-if command -v rsync >/dev/null 2>&1; then
+if [[ "$INSTALL_MODE" == "keep" ]]; then
-  rsync -a --delete "$SOURCE_DIR/" "$TARGET_DIR/"
+  ok "Install mode: keep local SOUL.md/memory while updating framework"
 else
-  rm -rf "$TARGET_DIR"/*
+  ok "Install mode: overwrite existing files"
-  cp -R "$SOURCE_DIR"/* "$TARGET_DIR"/
 fi
 
+sync_framework
+
 chmod +x "$TARGET_DIR"/bin/*
 chmod +x "$TARGET_DIR"/install.sh
 

remote-install.ps1

@@ -8,12 +8,13 @@
 #
 $ErrorActionPreference = "Stop"
 
-$ArchiveUrl = "https://git.mosaicstack.dev/mosaic/bootstrap/archive/main.zip"
+$BootstrapRef = if ($env:MOSAIC_BOOTSTRAP_REF) { $env:MOSAIC_BOOTSTRAP_REF } else { "main" }
+$ArchiveUrl = "https://git.mosaicstack.dev/mosaic/bootstrap/archive/$BootstrapRef.zip"
 $WorkDir = Join-Path $env:TEMP "mosaic-bootstrap-$PID"
 $ZipPath = "$WorkDir.zip"
 
 try {
-    Write-Host "[mosaic] Downloading bootstrap archive..."
+    Write-Host "[mosaic] Downloading bootstrap archive (ref: $BootstrapRef)..."
     New-Item -ItemType Directory -Path $WorkDir -Force | Out-Null
     Invoke-WebRequest -Uri $ArchiveUrl -OutFile $ZipPath -UseBasicParsing
 

remote-install.sh

@@ -9,7 +9,8 @@
 #
 set -eu
 
-ARCHIVE_URL="https://git.mosaicstack.dev/mosaic/bootstrap/archive/main.tar.gz"
+BOOTSTRAP_REF="${MOSAIC_BOOTSTRAP_REF:-main}"
+ARCHIVE_URL="https://git.mosaicstack.dev/mosaic/bootstrap/archive/${BOOTSTRAP_REF}.tar.gz"
 TMPDIR_BASE="${TMPDIR:-/tmp}"
 WORK_DIR="$TMPDIR_BASE/mosaic-bootstrap-$$"
 
@@ -18,7 +19,7 @@ cleanup() {
 }
 trap cleanup EXIT
 
-echo "[mosaic] Downloading bootstrap archive..."
+echo "[mosaic] Downloading bootstrap archive (ref: $BOOTSTRAP_REF)..."
 
 mkdir -p "$WORK_DIR"