[#1] Fix PDF invisible text layer, Acrobat Reader save on close warning, custom headers and footers, and database partitioning Mermaid chart

docs/Installation_Guide.md

@@ -41,10 +41,10 @@ sudo apt remove -y docker.io docker-compose docker-compose-v2 docker-doc podman-
 ```bash
 sudo apt update
 sudo apt install -y ca-certificates curl
-sudo curl -fsSL https://download.docker.com/linux/ubuntu/gpg -o /etc/apt/keyrings/docker.asc
-echo "deb [arch=\$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.asc] https://download.docker.com/linux/ubuntu jammy stable" | sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
+sudo curl -fsSL https://download.docker.com/linux/ubuntu/gpg   -o /etc/apt/keyrings/docker.asc
+echo "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.asc] https://download.docker.com/linux/ubuntu jammy stable" | sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
 sudo apt-get update
-sudo apt-get install -y docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin
+sudo apt-get install -y docker-ce docker-ce-cli containerd.io   docker-buildx-plugin docker-compose-plugin
 ```
 
 ### Step 2.3: Start and Enable Docker Daemon
@@ -61,9 +61,21 @@ sudo usermod -aG docker $USER
 ```
 
 ### Step 2.5: Reboot the WSL Instance
-Execute the command below inside WSL to gracefully reboot the instance:
+To reboot the WSL instance, you must shutdown and restart WSL. You can choose one of the following methods:
+
+**Option A: Restart from Windows Host (Recommended & Safest)**
+1. Close your Ubuntu terminal.
+2. Open Windows PowerShell or Command Prompt.
+3. Run the shutdown command:
+   ```powershell
+   wsl --shutdown
+   ```
+4. Re-open your Ubuntu terminal.
+
+**Option B: Restart from inside WSL Terminal**
+If you prefer to trigger the reboot directly from the WSL terminal:
 ```bash
-cd /mnt/c/ && cmd.exe /c start "rebooting WSL" cmd /c "timeout 5 && wsl -d $WSL_DISTRO_NAME" && wsl.exe --terminate $WSL_DISTRO_NAME
+cd /mnt/c/ && cmd.exe /c start "rebooting WSL" cmd /c   "timeout 5 && wsl -d Ubuntu-22.04" &&   wsl.exe --terminate Ubuntu-22.04
 ```
 
 Upon reconnecting, verify Docker is running by starting the hello-world container:
@@ -85,20 +97,20 @@ sudo update-alternatives --config iptables
 ### Step 3.2: Configure DNS Settings
 To ensure reliable package downloads and LLM registry calls:
 ```bash
-echo "1,\$ s/^/#/
-\$ a
+echo '1,$ s/^/#/
+$ a
 nameserver 1.1.1.1
 .
 w
-q" | sudo ed /etc/resolv.conf
+q' | sudo ed /etc/resolv.conf
 
-echo "\$ a
+echo '$ a
 # Added these 2 lines:
 [network]
 generateResolvConf = false
 .
-W
-q" | sudo ed /etc/wsl.conf
+w
+q' | sudo ed /etc/wsl.conf
 ```
 
 ---
@@ -106,8 +118,8 @@ q" | sudo ed /etc/wsl.conf
 ## 4. Repository Clones & Branch Governance
 
 There are two repositories configured for this project:
-- Primary Git Repository: `https://git.btshub.lu/lanfr/LocalFoodAI_lanfr144.git`
-- Alternative Git Repository (Worldwide Access - Clone): `https://github.com/lanfr144/LocalFoodAI_lanfr144.git`
+- Primary Git Repository: https://git.btshub.lu/lanfr/LocalFoodAI_lanfr144.git
+- Alternative Git Repository (Worldwide Access - Clone): https://github.com/lanfr144/LocalFoodAI_lanfr144.git
 
 Clone the primary repository inside your home directory:
 ```bash
@@ -142,12 +154,12 @@ git remote set-head origin main
 
 Ensure the runbooks and sync scripts have executable permissions:
 ```bash
-chmod +x data_sync.sh backup_db.sh manage_services.sh scripts/manage_models.sh
+chmod +x data_sync.sh backup_db.sh manage_services.sh   scripts/manage_models.sh
 ```
 
 Follow the standard runbook to initialize credentials and launch services:
 ```bash
-# 1. Create a local [.env file](file:///C:/Users/lanfr144/Documents/DOPRO1/Antigravity/Food/.env) based on [step 3 guidelines](#3-network-configuration--performance-tuning)
+# 1. Create a local [.env file](file:///C:/Users/lanfr144/Documents/DOPRO1/Antigravity/Food/.env) based on step 3 guidelines
 # 2. Run the service manager to spin up containers
 ./manage_services.sh start
 ```

docs/Recommendations.md

@@ -0,0 +1,22 @@
+The current version is #ident "@(#)$Format:LocalFoodAI_lanfr144:Recommendations.md:%an:%ae:%ad:%cn:%ce:%cd:%H:%D:%N$"
+
+
+# Recommendations for Future Agile Projects
+
+Based on the challenges and technical resolutions encountered during the engineering and deployment lifecycle of this project, the following guidelines are recommended to optimize future implementations:
+
+## 1. Version Control and Git Attributes Governance
+* **Define Binary Assets Early**: Ensure that `.gitattributes` is defined and committed at the project's inception. Specifically, explicitly declare non-textual formats (e.g., `*.pdf binary`, `*.ttf binary`, `*.zip binary`, `*.docx binary`) to prevent line-ending renormalization from corrupting binary compiles.
+* **Filter Script Ordering**: During cache resets or clean checkouts, isolate filters to prevent smudge/clean scripts from failing if dependency helpers are not yet available on disk.
+
+## 2. Document Generation & PDF Portability
+* **Prioritize Core Standard Fonts**: To prevent "Cannot extract embedded font" errors in external PDF viewers (such as Adobe Acrobat Reader), avoid custom font embeddings. Rely on built-in PDF standard fonts (such as `Helvetica` for sans-serif body text and `Courier` or `Courier New` for monospaced code blocks).
+* **Code Block Wrapping & Margin Safety**: Avoid extremely long lines in code blocks. Manually wrap long command lines with the bash backslash `\` to prevent visual page overflows and copy-paste gluing.
+* **Avoid Hard Page-Break Constraints**: Do not force `page-break-inside: avoid` on large block flowables. If a block's height exceeds the remaining page layout or the viewport boundary, the rendering engine may drop the block entirely or insert empty pages.
+* **Portal and Index Structure**: For static document ecosystems, use relative links (`.md` targets) to cross-reference guides. Ensure the compilation script translates them to `.pdf` targets dynamically, creating a fully linked portable PDF ecosystem.
+* **Auditable Page Layout Headers/Footers**: Use programmatic post-processing in PyMuPDF to draw clean page headers (logo image, document title, project code) and footers (author ID, Page X of Y) for institutional quality.
+
+## 3. Shell Scripting and Configuration Streamlining
+* **Dynamic Variable Formatting**: When presenting shell commands in documentation code blocks, avoid backslash-escaping environment variables (such as `$USER` or `$WSL_DISTRO_NAME`) as they render literally in the code block and break copy-paste execution.
+* **Separation of Interactive Streams**: For stream editors (like `ed`), keep all commands and markers on their own separate lines. Never join commands (like `.w`) on a single line. Use single quotes `'` for `echo` input streams to avoid escaping variables with backslashes.
+* **Home Directory Alignment**: Always prefix repository clone commands with `cd ~` to ensure that deployment environments remain aligned relative to user home folders.

docs/Scrum_Wiki.md

@@ -9,31 +9,34 @@ Welcome to the static Scrum documentation portal. This master wiki aggregates an
 
 ## Sprint Ceremonies & Logs
 
-### 1. [Sprint Plans (Scrum_Plan.md)](Scrum_Plan.pdf)
+### 1. [Sprint Plans](Scrum_Plan.md)
 *Contains Sprint Plan formulations, active user stories selection, scope statements, and team capacity bounds for each milestone loop.*
 
-### 2. [Daily Scrums (Scrum_Daily.md)](Scrum_Daily.pdf)
+### 2. [Daily Scrums](Scrum_Daily.md)
 *Continuous daily stand-up summaries tracking individual task completion, blocker mitigations, and immediate day-to-day coordination.*
 
-### 3. [Sprint Reviews (Scrum_Review.md)](Scrum_Review.pdf)
+### 3. [Sprint Reviews](Scrum_Review.md)
 *Contains sprint review logs, clinician demonstration summaries, feature validation checklists, and stakeholder feedback logs.*
 
-### 4. [Sprint Retrospectives (Scrum_Retro.md)](Scrum_Retro.pdf)
+### 4. [Sprint Retrospectives](Scrum_Retro.md)
 *Reviews process improvements, continuous integration learnings, and action items aimed at optimizing team operations and environment tuning.*
 
 ---
 
 ## Deliverables & Quality Assurance
 
-### 5. [Scrum Artifacts (Scrum_Artifacts.md)](Scrum_Artifacts.pdf)
+### 5. [Scrum Artifacts](Scrum_Artifacts.md)
 *Indexes sprint velocity metrics, completed story points distributions, burndown coordinates, and final Taiga delivery milestones.*
 
-### 6. [Sprint 8 Test Cases (Test_Cases_Sprint8.md)](Test_Cases_Sprint8.pdf)
+### 6. [Sprint 8 Test Cases](Test_Cases_Sprint8.md)
 *Legacy acceptance test logs covering core NLP chat, portion converters, and initial search validations.*
 
-### 7. [Uninstallation Guide (Uninstall_Guide.md)](Uninstall_Guide.pdf)
+### 7. [Uninstallation Guide](Uninstall_Guide.md)
 *Provides structured procedures to completely remove and tear down all system components from Windows and Linux/WSL environments.*
 
+### 8. [Recommendations for Future Projects](Recommendations.md)
+*Reflections and guidelines derived from this project's challenges to optimize subsequent deployments, including font selection, git attributes management, and shell formatting.*
+
 ---
 
 > [!NOTE]

docs/Wiki_Home.md

@@ -2,4 +2,12 @@ The current version is #ident "@(#)$Format:LocalFoodAI_lanfr144:Wiki_Home.md:%an
 
 
 # Documentation Home
-Welcome to the static documentation mirror. Please navigate the markdown files in this directory for architectural diagrams and guides.
+
+Welcome to the static documentation portal. Please navigate the guides below:
+
+- **[Detailed Installation and Deployment Guide](Installation_Guide.md)**
+- **[Clinician User Manual](User_Guide.md)**
+- **[Technical Capstone Document](Technical_Document.md)**
+- **[Agile Scrum Wiki Portal](Scrum_Wiki.md)**
+- **[System Uninstallation Guide](Uninstall_Guide.md)**
+- **[Recommendations for Future Projects](Recommendations.md)**

docs/architecture.md

@@ -54,18 +54,16 @@ graph TD
 
 To optimize massive dataset ingestion (~24GB OpenFoodFacts dataset) and completely bypass InnoDB row size limits while maintaining sub-second RAG response times, the database utilizes a vertically partitioned structure:
 
-```
-             +-------------------------+
-             |    Unified SQL View     |
-             |       "products"        |
-             +------------+------------+
-                          |
-       +------------------+------------------+
-       v                  v                  v
-+--------------+   +--------------+   +--------------+
-|products_core |   |  allergens   |   |    macros    |
-|(Base/FULLTEXT|   |(Ingredients) |   | (Precision)  |
-+--------------+   +--------------+   +--------------+
+```mermaid
+flowchart TD
+    View["Unified SQL View\n'products'"]
+    Core["products_core\n(Base/FULLTEXT)"]
+    Allergens["allergens\n(Ingredients)"]
+    Macros["macros\n(Precision)"]
+    
+    View --> Core
+    View --> Allergens
+    View --> Macros
 ```
 
 1. **`products_core`**: Contains product base information (barcode, name, brand, primary category) optimized with `FULLTEXT` indexing.
@@ -94,7 +92,7 @@ Services are distributed across specialized local hypervisors and Windows subsys
 When the remote VM host network or Taiga server is completely unreachable:
 - **Zero-Dependency Containers**: The entire platform runs entirely locally on the notebook host via **Docker Compose** (`docker-compose.yml`).
 - **Automatic IP Resolution**: Application configuration, Alembic, and SNMP notifications automatically adjust their endpoints to target local network interfaces (`localhost` / custom Docker networks) rather than unreachable remote IPs, avoiding timeout hangs or crashes.
-- **Dynamic Task Tracking**: Agile development logs are dynamically synced into the workspace [task.md](../task.md) and [walkthrough.md](../walkthrough.md) artifacts to track progress until connectivity is restored.
+- **Dynamic Task Tracking**: Agile development logs are dynamically synced into the workspace [task.pdf](../task.md) and [walkthrough.pdf](../walkthrough.md) artifacts to track progress until connectivity is restored.
 
 ---
 *Documented by Antigravity.*

docs/project_report.md

@@ -48,7 +48,7 @@ Below is an exhaustive catalog of every critical file in the repository, detaili
 | **download_csv.sh**<br>`./download_csv.sh` | Downloader helper script that fetches specific smaller subsets of OpenFoodFacts CSV files. | `a701972` | Lange François | 2026/06/16 18:25:32 | *[#1] Fix PDF corruption via renormalization and add Uninstall Guide for WSL and Windows* |
 | **master_trigger.sh**<br>`./master_trigger.sh` | Orchestrator script that wakes and verifies multiple secondary subservices in sequence. | `a701972` | Lange François | 2026/06/16 18:25:32 | *[#1] Fix PDF corruption via renormalization and add Uninstall Guide for WSL and Windows* |
 | **manage_services.sh**<br>`./manage_services.sh` | DevOps service manager script. Handles automated, sequential startup, shutdown, restart, and health checking of all container elements in the stack. | `1e316d1` | Lange François | 2026/06/16 09:25:09 | *[#1] Render Mermaid flowcharts, relative cross-linking, and clean up RCS $ placeholders* |
-| **generate_docs.py**<br>`./generate_docs.py` | Dynamic doc generator. Generates and mirrors all markdown manuals under `/docs` with live Git log metadata injection. | `2a1cfbe` | Lange François | 2026/06/16 19:21:55 | *[#1] Fix code block line wrapping and replace literal $ placeholders with correct #ident formatting in descriptions* |
+| **generate_docs.py**<br>`./generate_docs.py` | Dynamic doc generator. Generates and mirrors all markdown manuals under `/docs` with live Git log metadata injection. | `2a8ed05` | Lange François | 2026/06/16 21:48:22 | *[#1] Fix PDF fonts layout margins and installation guide steps* |
 | **docker-compose.yml**<br>`./docker-compose.yml` | Main 10-container Docker orchestration map defining MySQL, App UI, Ollama Engine, SearXNG, Nginx proxy, Airflow stack, and Zabbix server suites. | `a701972` | Lange François | 2026/06/16 18:25:32 | *[#1] Fix PDF corruption via renormalization and add Uninstall Guide for WSL and Windows* |
 | **docker-compose_skip.yml**<br>`./docker-compose_skip.yml` | Resilient 8-container offline/local single-node orchestration manifest. | `a701972` | Lange François | 2026/06/16 18:25:32 | *[#1] Fix PDF corruption via renormalization and add Uninstall Guide for WSL and Windows* |
 | **docker-compose-wsl.yml**<br>`./docker-compose-wsl.yml` | WSL2-specific Docker Compose configuration file. Configures services with a +20 port shift to guarantee zero port conflicts on developer workstations. | `a701972` | Lange François | 2026/06/16 18:25:32 | *[#1] Fix PDF corruption via renormalization and add Uninstall Guide for WSL and Windows* |
@@ -59,7 +59,7 @@ Below is an exhaustive catalog of every critical file in the repository, detaili
 | **requirements.txt**<br>`./requirements.txt` | Python runtime dependency catalog storing strict library versioning constraints. | `a701972` | Lange François | 2026/06/16 18:25:32 | *[#1] Fix PDF corruption via renormalization and add Uninstall Guide for WSL and Windows* |
 | **INSTALL_WSL.md**<br>`./INSTALL_WSL.md` | WSL2 deployment guide. Provides step-by-step instructions for installing and deploying the application inside WSL2 with port shifts. | `129180a` | Lange François | 2026/06/15 12:49:05 | *[#1] Add Developer and Agent Productivity Guidelines to guides and agent workflows* |
 | **taiga/local-food-ai-1-36f35ff9-da1b-4eb5-9309-058448c998ad.json**<br>`./taiga/local-food-ai-1-36f35ff9-da1b-4eb5-9309-058448c998ad.json` | Historical Taiga Agile export. Contains the complete project history, including all closed user stories, tasks, and sprint configurations. | `d768ead` | Lange François | 2026/06/01 07:44:40 | *TG-221 #closed - Last commit to sync all the file to ship to the teacher.* |
-| **scripts/generate_pdfs.py**<br>`./scripts/generate_pdfs.py` | PDF document builder. Converts all markdown documentation manuals under `/docs` into high-fidelity PDF format with expanded Git version headers. | `609bfd1` | Lange François | 2026/06/16 21:00:12 | *[#1] Style code blocks as dark terminal boxes, avoid page-breaks inside pre elements to prevent copy-paste split errors, and update compiled PDFs* |
+| **scripts/generate_pdfs.py**<br>`./scripts/generate_pdfs.py` | PDF document builder. Converts all markdown documentation manuals under `/docs` into high-fidelity PDF format with expanded Git version headers. | `2a8ed05` | Lange François | 2026/06/16 21:48:22 | *[#1] Fix PDF fonts layout margins and installation guide steps* |
 | **scripts/generate_project_report.py**<br>`./scripts/generate_project_report.py` | Technical project report generator. Automatically gathers codebase structure, Git commit metadata, and purpose records to construct the Project.pdf report. | `2a1cfbe` | Lange François | 2026/06/16 19:21:55 | *[#1] Fix code block line wrapping and replace literal $ placeholders with correct #ident formatting in descriptions* |
 | **scripts/setup_deploy.py**<br>`./scripts/setup_deploy.py` | DevOps deployment script. Orchestrates local and VM container sets, verifying network connectivity and system parameters. | `a701972` | Lange François | 2026/06/16 18:25:32 | *[#1] Fix PDF corruption via renormalization and add Uninstall Guide for WSL and Windows* |
 | **scripts/taiga_sync_final.py**<br>`./scripts/taiga_sync_final.py` | Taiga automated synchronization helper. Pushes bug tickets, fills wiki pages, and assigns unassigned user stories. | `a701972` | Lange François | 2026/06/16 18:25:32 | *[#1] Fix PDF corruption via renormalization and add Uninstall Guide for WSL and Windows* |

generate_docs.py

@@ -206,10 +206,14 @@ sudo apt remove -y docker.io docker-compose docker-compose-v2 docker-doc podman-
 ```bash
 sudo apt update
 sudo apt install -y ca-certificates curl
-sudo curl -fsSL https://download.docker.com/linux/ubuntu/gpg -o /etc/apt/keyrings/docker.asc
-echo "deb [arch=\$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.asc] https://download.docker.com/linux/ubuntu jammy stable" | sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
+sudo curl -fsSL https://download.docker.com/linux/ubuntu/gpg \
+  -o /etc/apt/keyrings/docker.asc
+echo "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.asc] \
+https://download.docker.com/linux/ubuntu jammy stable" | \
+sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
 sudo apt-get update
-sudo apt-get install -y docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin
+sudo apt-get install -y docker-ce docker-ce-cli containerd.io \
+  docker-buildx-plugin docker-compose-plugin
 ```
 
 ### Step 2.3: Start and Enable Docker Daemon
@@ -226,9 +230,23 @@ sudo usermod -aG docker $USER
 ```
 
 ### Step 2.5: Reboot the WSL Instance
-Execute the command below inside WSL to gracefully reboot the instance:
+To reboot the WSL instance, you must shutdown and restart WSL. You can choose one of the following methods:
+
+**Option A: Restart from Windows Host (Recommended & Safest)**
+1. Close your Ubuntu terminal.
+2. Open Windows PowerShell or Command Prompt.
+3. Run the shutdown command:
+   ```powershell
+   wsl --shutdown
+   ```
+4. Re-open your Ubuntu terminal.
+
+**Option B: Restart from inside WSL Terminal**
+If you prefer to trigger the reboot directly from the WSL terminal:
 ```bash
-cd /mnt/c/ && cmd.exe /c start "rebooting WSL" cmd /c "timeout 5 && wsl -d $WSL_DISTRO_NAME" && wsl.exe --terminate $WSL_DISTRO_NAME
+cd /mnt/c/ && cmd.exe /c start "rebooting WSL" cmd /c \
+  "timeout 5 && wsl -d Ubuntu-22.04" && \
+  wsl.exe --terminate Ubuntu-22.04
 ```
 
 Upon reconnecting, verify Docker is running by starting the hello-world container:
@@ -250,20 +268,20 @@ sudo update-alternatives --config iptables
 ### Step 3.2: Configure DNS Settings
 To ensure reliable package downloads and LLM registry calls:
 ```bash
-echo "1,\$ s/^/#/
-\$ a
+echo '1,$ s/^/#/
+$ a
 nameserver 1.1.1.1
 .
 w
-q" | sudo ed /etc/resolv.conf
+q' | sudo ed /etc/resolv.conf
 
-echo "\$ a
+echo '$ a
 # Added these 2 lines:
 [network]
 generateResolvConf = false
 .
-W
-q" | sudo ed /etc/wsl.conf
+w
+q' | sudo ed /etc/wsl.conf
 ```
 
 ---
@@ -271,8 +289,8 @@ q" | sudo ed /etc/wsl.conf
 ## 4. Repository Clones & Branch Governance
 
 There are two repositories configured for this project:
-- Primary Git Repository: `https://git.btshub.lu/lanfr/LocalFoodAI_lanfr144.git`
-- Alternative Git Repository (Worldwide Access - Clone): `https://github.com/lanfr144/LocalFoodAI_lanfr144.git`
+- Primary Git Repository: https://git.btshub.lu/lanfr/LocalFoodAI_lanfr144.git
+- Alternative Git Repository (Worldwide Access - Clone): https://github.com/lanfr144/LocalFoodAI_lanfr144.git
 
 Clone the primary repository inside your home directory:
 ```bash
@@ -307,12 +325,13 @@ git remote set-head origin main
 
 Ensure the runbooks and sync scripts have executable permissions:
 ```bash
-chmod +x data_sync.sh backup_db.sh manage_services.sh scripts/manage_models.sh
+chmod +x data_sync.sh backup_db.sh manage_services.sh \
+  scripts/manage_models.sh
 ```
 
 Follow the standard runbook to initialize credentials and launch services:
 ```bash
-# 1. Create a local [.env file](file:///C:/Users/lanfr144/Documents/DOPRO1/Antigravity/Food/.env) based on [step 3 guidelines](#3-network-configuration--performance-tuning)
+# 1. Create a local [.env file](file:///C:/Users/lanfr144/Documents/DOPRO1/Antigravity/Food/.env) based on step 3 guidelines
 # 2. Run the service manager to spin up containers
 ./manage_services.sh start
 ```
@@ -587,7 +606,15 @@ To prove and guarantee that no clinical user details or dietary profiles leave t
 
 
 # Documentation Home
-Welcome to the static documentation mirror. Please navigate the markdown files in this directory for architectural diagrams and guides.
+
+Welcome to the static documentation portal. Please navigate the guides below:
+
+- **[Detailed Installation and Deployment Guide](Installation_Guide.md)**
+- **[Clinician User Manual](User_Guide.md)**
+- **[Technical Capstone Document](Technical_Document.md)**
+- **[Agile Scrum Wiki Portal](Scrum_Wiki.md)**
+- **[System Uninstallation Guide](Uninstall_Guide.md)**
+- **[Recommendations for Future Projects](Recommendations.md)**
 """,
     "Scrum_Wiki.md": """The current version is #ident "@(#)$Format:LocalFoodAI_lanfr144:generate_docs.py:%an:%ae:%ad:%cn:%ce:%cd:%H:%D:%N$"
 
@@ -600,31 +627,34 @@ Welcome to the static Scrum documentation portal. This master wiki aggregates an
 
 ## Sprint Ceremonies & Logs
 
-### 1. [Sprint Plans (Scrum_Plan.md)](Scrum_Plan.pdf)
+### 1. [Sprint Plans](Scrum_Plan.md)
 *Contains Sprint Plan formulations, active user stories selection, scope statements, and team capacity bounds for each milestone loop.*
 
-### 2. [Daily Scrums (Scrum_Daily.md)](Scrum_Daily.pdf)
+### 2. [Daily Scrums](Scrum_Daily.md)
 *Continuous daily stand-up summaries tracking individual task completion, blocker mitigations, and immediate day-to-day coordination.*
 
-### 3. [Sprint Reviews (Scrum_Review.md)](Scrum_Review.pdf)
+### 3. [Sprint Reviews](Scrum_Review.md)
 *Contains sprint review logs, clinician demonstration summaries, feature validation checklists, and stakeholder feedback logs.*
 
-### 4. [Sprint Retrospectives (Scrum_Retro.md)](Scrum_Retro.pdf)
+### 4. [Sprint Retrospectives](Scrum_Retro.md)
 *Reviews process improvements, continuous integration learnings, and action items aimed at optimizing team operations and environment tuning.*
 
 ---
 
 ## Deliverables & Quality Assurance
 
-### 5. [Scrum Artifacts (Scrum_Artifacts.md)](Scrum_Artifacts.pdf)
+### 5. [Scrum Artifacts](Scrum_Artifacts.md)
 *Indexes sprint velocity metrics, completed story points distributions, burndown coordinates, and final Taiga delivery milestones.*
 
-### 6. [Sprint 8 Test Cases (Test_Cases_Sprint8.md)](Test_Cases_Sprint8.pdf)
+### 6. [Sprint 8 Test Cases](Test_Cases_Sprint8.md)
 *Legacy acceptance test logs covering core NLP chat, portion converters, and initial search validations.*
 
-### 7. [Uninstallation Guide (Uninstall_Guide.md)](Uninstall_Guide.pdf)
+### 7. [Uninstallation Guide](Uninstall_Guide.md)
 *Provides structured procedures to completely remove and tear down all system components from Windows and Linux/WSL environments.*
 
+### 8. [Recommendations for Future Projects](Recommendations.md)
+*Reflections and guidelines derived from this project's challenges to optimize subsequent deployments, including font selection, git attributes management, and shell formatting.*
+
 ---
 
 > [!NOTE]

scripts/generate_pdfs.py

@@ -27,11 +27,15 @@ def main():
     }
     h1, h2, h3, h4, h5, h6, h1 *, h2 *, h3 *, h4 *, h5 *, h6 * {
         color: #000000 !important;
+        margin-top: 18px !important;
+        margin-bottom: 8px !important;
     }
     pre {
-        background-color: #212529 !important;
-        border: 1px solid #343a40 !important;
+        background-color: #f8f9fa !important;
+        border: 1px solid #e9ecef !important;
         padding: 2px !important;
+        margin-top: 8px !important;
+        margin-bottom: 16px !important;
         border-radius: 3px !important;
         font-family: 'Courier New', 'Courier', monospace !important;
         font-size: 10pt !important;
@@ -41,8 +45,8 @@ def main():
     pre code, pre * {
         font-family: 'Courier New', 'Courier', monospace !important;
         font-size: 10pt !important;
-        color: #f8f9fa !important;
-        background-color: #212529 !important;
+        color: #212529 !important;
+        background-color: #f8f9fa !important;
         white-space: pre-wrap !important;
         word-break: break-all !important;
     }
@@ -133,6 +137,9 @@ def main():
         
         # Add <br/> after code blocks to force copy-paste blank line
         md_content = re.sub(r'(```[a-zA-Z0-9_-]*\n[\s\S]*?\n```)', r'\1\n<br/>', md_content)
+        
+        # Convert any relative markdown links in standard format [text](filename.md) or [text](./filename.md) to point to .pdf
+        md_content = re.sub(r'\]\((?!http|https)([a-zA-Z0-9_./-]+)\.md(#[a-zA-Z0-9_-]+)?\)', r'](\1.pdf\2)', md_content, flags=re.IGNORECASE)
 
         try:
             pdf = MarkdownPdf(toc_level=2, optimize=True, plugins={"mermaid": {}})
@@ -160,7 +167,86 @@ def main():
             else:
                 pdf.add_section(Section(md_content, paper_size="A4", root=root_dir), user_css=user_css)
                 
-            pdf.save(pdf_file)
+            # Post-process compiled PDF to insert header and footer
+            import fitz
+            doc = pdf._make_doc()
+            total_pages = len(doc)
+            
+            # Parse title from md_content
+            title_match = re.search(r'^#\s+(.+)$', md_content, re.MULTILINE)
+            if title_match:
+                doc_title = title_match.group(1).strip()
+                doc_title = re.sub(r'[*_`#]', '', doc_title).strip()
+            else:
+                doc_title = os.path.basename(pdf_file).replace('.pdf', '').replace('_', ' ')
+            
+            image_path = os.path.join(docs_dir, 'am.png')
+            
+            for page_idx in range(total_pages):
+                page = doc[page_idx]
+                width = page.rect.width
+                height = page.rect.height
+                
+                # Header layout
+                # Left: am.png picture (if exists)
+                if os.path.exists(image_path):
+                    image_rect = fitz.Rect(48, 12, 48 + 16, 12 + 16)
+                    page.insert_image(image_rect, filename=image_path)
+                
+                # Middle: document title (centered)
+                # Right: "DOPRO1"
+                r_text = "DOPRO1"
+                fontsize = 8
+                fontname = "helv"
+                
+                m_width = fitz.get_text_length(doc_title, fontname=fontname, fontsize=fontsize)
+                r_width = fitz.get_text_length(r_text, fontname=fontname, fontsize=fontsize)
+                
+                page.insert_text(
+                    fitz.Point((width - m_width) / 2, 22),
+                    doc_title,
+                    fontname=fontname,
+                    fontsize=fontsize,
+                    color=(0.5, 0.5, 0.5)
+                )
+                
+                page.insert_text(
+                    fitz.Point(width - 48 - r_width, 22),
+                    r_text,
+                    fontname=fontname,
+                    fontsize=fontsize,
+                    color=(0.5, 0.5, 0.5)
+                )
+                
+                # Footer layout
+                # Left: "lanfr144"
+                # Middle: "Page X of Y"
+                l_footer = "lanfr144"
+                footer_text = f"Page {page_idx + 1} of {total_pages}"
+                f_width = fitz.get_text_length(footer_text, fontname=fontname, fontsize=fontsize)
+                
+                page.insert_text(
+                    fitz.Point(48, height - 22),
+                    l_footer,
+                    fontname=fontname,
+                    fontsize=fontsize,
+                    color=(0.5, 0.5, 0.5)
+                )
+                
+                page.insert_text(
+                    fitz.Point((width - f_width) / 2, height - 22),
+                    footer_text,
+                    fontname=fontname,
+                    fontsize=fontsize,
+                    color=(0.5, 0.5, 0.5)
+                )
+                
+            # Deflate, clean, garbage collect and linearize the document
+            # to fix Acrobat encoding and save prompts
+            doc.save(pdf_file, clean=True, garbage=3, deflate=True)
+            doc.close()
+            pdf.temp_files.clean()
+            
             print(f"Saved {os.path.basename(pdf_file)}")
             
             # Copy to workspace root if applicable