diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
index 92a87c1..5e9c05b 100644
--- a/.github/copilot-instructions.md
+++ b/.github/copilot-instructions.md
@@ -26,7 +26,16 @@ Read [`LIBRARIAN.md`](../LIBRARIAN.md) before navigating the collections. It exp
 ## Tools
 
 ```bash
+# Full reconstruction from a clean clone (configure .env first)
+./bootstrap.sh
+
+# Restore cloud-storage symlinks only
+./init-symlinks.sh
+
+# Download PDFs from an archive page
 python3 download.py "URL" --output-dir collections/NAME/pdfs
+
+# Convert PDFs to searchable Markdown
 python3 convert.py --input-dir collections/NAME/pdfs --output-dir collections/NAME/indexed
 ```
 
diff --git a/AGENTS.md b/AGENTS.md
index 0e04e82..c0451d4 100644
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -26,7 +26,16 @@ Read [`LIBRARIAN.md`](LIBRARIAN.md) before navigating the collections. It explai
 ## Tools
 
 ```bash
+# Full reconstruction from a clean clone (configure .env first)
+./bootstrap.sh
+
+# Restore cloud-storage symlinks only
+./init-symlinks.sh
+
+# Download PDFs from an archive page
 python3 download.py "URL" --output-dir collections/NAME/pdfs
+
+# Convert PDFs to searchable Markdown
 python3 convert.py --input-dir collections/NAME/pdfs --output-dir collections/NAME/indexed
 ```
 
diff --git a/CLAUDE.md b/CLAUDE.md
index 8a5679c..b788d0f 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -32,7 +32,8 @@ publication-library/
 ├── convert.py                    ← convert PDFs → markdown + page PNGs
 ├── search.py                     ← search across indexed collections with formatted output
 ├── init-findings.sh              ← scaffold the findings/ directory
-├── init-symlinks.sh              ← recreate cloud-storage symlinks (configure via .env)
+├── init-symlinks.sh              ← recreate cloud-storage symlinks (auto-derived from collections/)
+├── bootstrap.sh                  ← full reconstruction pipeline from a clean clone
 ├── .env.template                 ← configuration template (copy to .env and set LIBRARY_BASE)
 ├── README.md
 ├── CLAUDE.md                     ← this file
@@ -76,9 +77,11 @@ publication-library/
 # Scaffold findings/ directory
 ./init-findings.sh
 
-# Set up cloud-storage symlinks (first time or new machine)
+# Full reconstruction from a clean clone (downloads, converts, catalogues)
 cp .env.template .env   # then edit .env and set LIBRARY_BASE
-# Edit the LINKS array in init-symlinks.sh for your collection layout
+./bootstrap.sh
+
+# Restore symlinks only (LINKS auto-derived from collections/; override via .env)
 ./init-symlinks.sh
 
 # Download from an archive page
diff --git a/GEMINI.md b/GEMINI.md
index f5dd1f1..f9059eb 100644
--- a/GEMINI.md
+++ b/GEMINI.md
@@ -26,7 +26,16 @@ Read [`LIBRARIAN.md`](LIBRARIAN.md) before navigating the collections. It explai
 ## Tools
 
 ```bash
+# Full reconstruction from a clean clone (configure .env first)
+./bootstrap.sh
+
+# Restore cloud-storage symlinks only
+./init-symlinks.sh
+
+# Download PDFs from an archive page
 python3 download.py "URL" --output-dir collections/NAME/pdfs
+
+# Convert PDFs to searchable Markdown
 python3 convert.py --input-dir collections/NAME/pdfs --output-dir collections/NAME/indexed
 ```
 
diff --git a/README.md b/README.md
index 67908d8..8d41745 100644
--- a/README.md
+++ b/README.md
@@ -42,7 +42,8 @@ Python 3.10+. No other dependencies.
 | `convert.py` | Convert a folder of PDFs to searchable Markdown with page images |
 | `search.py` | Search across all indexed collections with grouped, formatted output |
 | `init-findings.sh` | Scaffold the `findings/` directory, with optional cloud storage symlink |
-| `init-symlinks.sh` | Recreate cloud-storage symlinks for PDFs, indexed output, and findings |
+| `init-symlinks.sh` | Recreate cloud-storage symlinks (auto-derived from `collections/`) |
+| `bootstrap.sh` | Full reconstruction pipeline: symlinks → download → convert → catalogue |
 
 ---
 
@@ -136,7 +137,7 @@ making everything available across multiple machines without committing copyrigh
 Both `collections/*/pdfs`, `collections/*/indexed`, and `findings/` are gitignored, so symlinks
 to cloud folders work seamlessly with version control.
 
-### Recommended folder layout
+### Recommended cloud folder layout
 
 A clean convention is to store each collection's PDFs in a named folder, and use `library-` prefixed
 folders for the derived library assets (indexed output and findings). For example, using Dropbox:
@@ -153,37 +154,43 @@ folders for the derived library assets (indexed output and findings). For exampl
 
 The `library-` prefix distinguishes library infrastructure from per-collection PDF archives at a glance.
 
-### Set up symlinks with init-symlinks.sh
+### One-command reconstruction with bootstrap.sh
 
-`init-symlinks.sh` automates symlink creation. Configure it once, then run it after every clone or
-on each new machine.
-
-**1. Set your library base path:**
+After cloning on a new machine, `bootstrap.sh` rebuilds the entire library in one step:
 
 ```bash
 cp .env.template .env
-# Edit .env and set LIBRARY_BASE to your cloud storage root, e.g.:
+# Edit .env — set LIBRARY_BASE to your cloud storage root, e.g.:
 # LIBRARY_BASE="${HOME}/Dropbox/my-library"
+
+./bootstrap.sh
 ```
 
-**2. Edit the `LINKS` array in `init-symlinks.sh`** to list your collections:
+This creates cloud directories, restores symlinks, downloads any missing PDFs (using the Source URL
+from each `COLLECTION.md`), converts them to searchable Markdown, and regenerates `CATALOGUE.md`.
+The script is idempotent — already-downloaded PDFs and already-converted output are skipped.
+
+### Symlinks only
+
+`init-symlinks.sh` restores symlinks without downloading or converting. Symlink targets are
+auto-derived from `collections/` using the naming convention above. To override, define a `LINKS`
+array in `.env`:
 
 ```bash
-declare -a LINKS=(
+# .env
+LINKS=(
     "findings:${LIBRARY_BASE}/library-findings"
     "collections/collection-a/pdfs:${LIBRARY_BASE}/collection-a"
     "collections/collection-a/indexed:${LIBRARY_BASE}/library-indexed/collection-a"
 )
 ```
 
-**3. Run it:**
+Then run:
 
 ```bash
 ./init-symlinks.sh
 ```
 
-The script is idempotent — safe to re-run; existing symlinks are skipped.
-
 ---
 
 ## Library catalogue
diff --git a/bootstrap.sh b/bootstrap.sh
new file mode 100755
index 0000000..d17cd95
--- /dev/null
+++ b/bootstrap.sh
@@ -0,0 +1,194 @@
+#!/usr/bin/env bash
+# bootstrap.sh — Full reconstruction pipeline for a publication-library instance.
+#
+# Reconstructs the complete library from a clean clone:
+#   1. Validates configuration (.env, LIBRARY_BASE)
+#   2. Initialises the lib/pfb submodule if needed
+#   3. Creates cloud-storage directories for each collection
+#   4. Runs init-symlinks.sh to restore local symlinks
+#   5. Downloads PDFs for each collection (skips if already present)
+#   6. Converts PDFs to searchable Markdown (skips if already done)
+#   7. Regenerates the cross-collection CATALOGUE.md
+#
+# Name:         bootstrap.sh
+# Description:  Full reconstruction pipeline for a publication-library instance
+# Author:       Alister Lewis-Bowen <alister@lewis-bowen.org>
+# Usage:        ./bootstrap.sh
+# Dependencies: bash 4+, python3, pymupdf, git, lib/pfb submodule
+# Exit codes:   0 success, 1 error
+#
+# Configuration (via .env or environment):
+#   LIBRARY_BASE  Absolute path to the root of your cloud-synced library storage.
+#                 See .env.template for examples.
+
+set -euo pipefail
+
+# ---------------------------------------------------------------------------
+# Bootstrap
+# ---------------------------------------------------------------------------
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+cd "${SCRIPT_DIR}"
+
+# Source .env if present
+if [[ -f "${SCRIPT_DIR}/.env" ]]; then
+    # shellcheck source=/dev/null
+    source "${SCRIPT_DIR}/.env"
+fi
+
+# Initialise lib/pfb submodule if not already done
+if [[ ! -f "${SCRIPT_DIR}/lib/pfb/pfb.sh" ]]; then
+    echo "Initialising lib/pfb submodule..."
+    git submodule update --init lib/pfb
+fi
+
+# Load pfb for terminal output
+# shellcheck source=lib/pfb/pfb.sh
+source "${SCRIPT_DIR}/lib/pfb/pfb.sh"
+
+# ---------------------------------------------------------------------------
+# Validate required configuration
+# ---------------------------------------------------------------------------
+
+pfb heading "publication-library bootstrap" "📚"
+echo
+
+if [[ ! -f "${SCRIPT_DIR}/.env" ]]; then
+    pfb error ".env not found."
+    pfb subheading "Copy .env.template to .env and set LIBRARY_BASE:"
+    pfb subheading "  cp .env.template .env"
+    exit 1
+fi
+
+if [[ -z "${LIBRARY_BASE:-}" ]]; then
+    pfb error "LIBRARY_BASE is not set in .env."
+    pfb subheading "Edit .env and set LIBRARY_BASE to your cloud storage root."
+    exit 1
+fi
+
+pfb info "LIBRARY_BASE: ${LIBRARY_BASE}"
+echo
+
+# ---------------------------------------------------------------------------
+# Helper: parse Source URL from a COLLECTION.md
+# @param $1  Path to COLLECTION.md
+# @return    Prints the source URL, or empty string if not found
+# ---------------------------------------------------------------------------
+parse_source_url() {
+    local col_md="${1}"
+    [[ -f "${col_md}" ]] || { echo ""; return; }
+    # Match:  | **Source** | [text](URL) |
+    local url
+    url="$(grep -oP '\|\s+\*\*Source\*\*\s+\|\s+\[[^\]]+\]\(\K[^)]+' "${col_md}" || true)"
+    echo "${url}"
+}
+
+# ---------------------------------------------------------------------------
+# Phase 1 — Create cloud-storage directories
+# ---------------------------------------------------------------------------
+
+pfb heading "Creating cloud-storage directories" "☁️"
+echo
+
+mkdir -p "${LIBRARY_BASE}/library-findings"
+pfb success "READY  ${LIBRARY_BASE}/library-findings"
+
+for col_dir in "${SCRIPT_DIR}/collections"/*/; do
+    [[ -d "${col_dir}" ]] || continue
+    name="$(basename "${col_dir}")"
+    mkdir -p "${LIBRARY_BASE}/${name}"
+    pfb success "READY  ${LIBRARY_BASE}/${name}"
+    mkdir -p "${LIBRARY_BASE}/library-indexed/${name}"
+    pfb success "READY  ${LIBRARY_BASE}/library-indexed/${name}"
+done
+
+echo
+
+# ---------------------------------------------------------------------------
+# Phase 2 — Restore symlinks
+# ---------------------------------------------------------------------------
+
+pfb heading "Restoring symlinks" "🔗"
+echo
+"${SCRIPT_DIR}/init-symlinks.sh"
+echo
+
+# ---------------------------------------------------------------------------
+# Phase 3 — Download PDFs
+# ---------------------------------------------------------------------------
+
+pfb heading "Downloading PDFs" "⬇️"
+echo
+
+for col_dir in "${SCRIPT_DIR}/collections"/*/; do
+    [[ -d "${col_dir}" ]] || continue
+    name="$(basename "${col_dir}")"
+    col_md="${col_dir}COLLECTION.md"
+
+    source_url="$(parse_source_url "${col_md}")"
+
+    if [[ -z "${source_url}" ]]; then
+        pfb warn "SKIP  ${name} — no Source URL in COLLECTION.md"
+        continue
+    fi
+
+    # Count PDFs already present (follow symlinks)
+    pdf_count="$(find -L "${col_dir}pdfs" -name "*.pdf" 2>/dev/null | wc -l | tr -d ' ')"
+    if [[ "${pdf_count}" -gt 0 ]]; then
+        pfb info "SKIP  ${name} — ${pdf_count} PDFs already present"
+        continue
+    fi
+
+    pfb subheading "${name} — downloading from ${source_url}"
+    python3 "${SCRIPT_DIR}/download.py" "${source_url}" \
+        --output-dir "collections/${name}/pdfs"
+    pfb success "DONE  ${name}"
+done
+
+echo
+
+# ---------------------------------------------------------------------------
+# Phase 4 — Convert PDFs to Markdown
+# ---------------------------------------------------------------------------
+
+pfb heading "Converting PDFs to Markdown" "📄"
+echo
+
+for col_dir in "${SCRIPT_DIR}/collections"/*/; do
+    [[ -d "${col_dir}" ]] || continue
+    name="$(basename "${col_dir}")"
+
+    # Skip if indexed output already exists and is non-empty
+    indexed_count="$(find -L "${col_dir}indexed" -name "index.md" 2>/dev/null | wc -l | tr -d ' ')"
+    if [[ "${indexed_count}" -gt 0 ]]; then
+        pfb info "SKIP  ${name} — already converted (${indexed_count} index files)"
+        continue
+    fi
+
+    # Skip if there are no PDFs to convert
+    pdf_count="$(find -L "${col_dir}pdfs" -name "*.pdf" 2>/dev/null | wc -l | tr -d ' ')"
+    if [[ "${pdf_count}" -eq 0 ]]; then
+        pfb warn "SKIP  ${name} — no PDFs found in collections/${name}/pdfs"
+        continue
+    fi
+
+    pfb subheading "${name} — converting ${pdf_count} PDFs"
+    python3 "${SCRIPT_DIR}/convert.py" \
+        --input-dir "collections/${name}/pdfs" \
+        --output-dir "collections/${name}/indexed" \
+        --pattern "**/*.pdf" \
+        --write-collection-md
+    pfb success "DONE  ${name}"
+done
+
+echo
+
+# ---------------------------------------------------------------------------
+# Phase 5 — Regenerate catalogue
+# ---------------------------------------------------------------------------
+
+pfb heading "Regenerating CATALOGUE.md" "🗂️"
+echo
+python3 "${SCRIPT_DIR}/convert.py" --global-index collections/
+echo
+pfb success "Done. Library reconstruction complete."
diff --git a/init-symlinks.sh b/init-symlinks.sh
index 57bb618..aa22556 100755
--- a/init-symlinks.sh
+++ b/init-symlinks.sh
@@ -16,11 +16,17 @@
 #   LIBRARY_BASE  Absolute path to the root of your cloud-synced library storage.
 #                 See .env.template for examples.
 #
-# LINKS format: "local_path:cloud_target"
-#   Edit the LINKS array below to match your instance's collection layout.
-#   - findings         → flat directory in cloud storage
-#   - COLLECTION/pdfs  → per-collection PDF directory in cloud storage
-#   - COLLECTION/indexed → per-collection indexed output under library-indexed/
+# LINKS are auto-derived from collections/*/ using the naming convention:
+#   collections/NAME/pdfs    → ${LIBRARY_BASE}/NAME
+#   collections/NAME/indexed → ${LIBRARY_BASE}/library-indexed/NAME
+#   findings                 → ${LIBRARY_BASE}/library-findings
+#
+# To override, define a LINKS array in .env before running:
+#   LINKS=(
+#     "findings:${LIBRARY_BASE}/library-findings"
+#     "collections/NAME/pdfs:${LIBRARY_BASE}/NAME"
+#     "collections/NAME/indexed:${LIBRARY_BASE}/library-indexed/NAME"
+#   )
 
 set -euo pipefail
 
@@ -31,7 +37,7 @@ set -euo pipefail
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 cd "${SCRIPT_DIR}"
 
-# Source .env if present (allows LIBRARY_BASE to be set there)
+# Source .env if present (allows LIBRARY_BASE and optional LINKS override to be set there)
 if [[ -f "${SCRIPT_DIR}/.env" ]]; then
     # shellcheck source=/dev/null
     source "${SCRIPT_DIR}/.env"
@@ -62,22 +68,25 @@ if [[ -z "${LIBRARY_BASE:-}" ]]; then
 fi
 
 # ---------------------------------------------------------------------------
-# Symlink definitions — edit to match your instance layout
+# Build LINKS — auto-derive from collections/*/ unless overridden in .env
 # ---------------------------------------------------------------------------
-# Format: "local_path:cloud_target"
-# local_path  — path relative to this script (e.g. findings, collections/NAME/pdfs)
-# cloud_target — absolute path under LIBRARY_BASE
-#
-# Example entries (uncomment and adapt):
-#
-#   "findings:${LIBRARY_BASE}/library-findings"
-#   "collections/my-collection/pdfs:${LIBRARY_BASE}/my-collection"
-#   "collections/my-collection/indexed:${LIBRARY_BASE}/library-indexed/my-collection"
 
-declare -a LINKS=(
-    # Add your symlink entries here. Example:
-    # "findings:${LIBRARY_BASE}/library-findings"
-)
+# @description Build the LINKS array from collections/*/ directories.
+# @side_effects Populates the global LINKS array.
+build_links() {
+    LINKS=()
+    LINKS+=("findings:${LIBRARY_BASE}/library-findings")
+    for col_dir in "${SCRIPT_DIR}/collections"/*/; do
+        [[ -d "${col_dir}" ]] || continue
+        name="$(basename "${col_dir}")"
+        LINKS+=("collections/${name}/pdfs:${LIBRARY_BASE}/${name}")
+        LINKS+=("collections/${name}/indexed:${LIBRARY_BASE}/library-indexed/${name}")
+    done
+}
+
+if [[ -z "${LINKS[*]+set}" ]] || [[ ${#LINKS[@]} -eq 0 ]]; then
+    build_links
+fi
 
 # ---------------------------------------------------------------------------
 # Main
@@ -88,7 +97,7 @@ pfb subheading "LIBRARY_BASE: ${LIBRARY_BASE}"
 echo
 
 if [[ ${#LINKS[@]} -eq 0 ]]; then
-    pfb warn "No symlinks defined. Edit the LINKS array in this script."
+    pfb warn "No collections found under collections/ and no LINKS defined in .env."
     exit 0
 fi