Update repository documentation and add offsetFit_MultipleLAPPD Script

.gitignore

@@ -0,0 +1,36 @@
+# Python
+__pycache__/
+*.pyc
+
+# C++ build artifacts
+*.o
+*.out
+*.exe
+
+# ROOT / analysis outputs
+*.root
+
+# ROOT dictionary files
+*.pcm
+*Dict.cxx
+*Dict.h
+
+# Libraries
+*.a
+*.so
+
+# macOS
+.DS_Store
+
+# IDE
+.vscode/
+
+# Automatic dependency files
+*.d
+
+# Core dumps
+core*
+
+# Editor backup files
+*~
+\#*#

README.md

@@ -1,4 +1,41 @@
-This repository is for standalone scripts.
-Place python scripts in the python directory, and c++ scripts in the cpp directory, and shell scripts in the bash directory.
-For c++, please include a Makefile to compile your application, unless it is to run as ROOT macro (though compiled scripts are preferred for compile-time error checking).
-For python scipts, please specify your environment and all python modules, including versions, your script relies on.
+# ANNIE Helper Scripts
+
+A repository for small standalone scripts that are detached from the ToolAnalysis. 
+For debugging, validation, ML training, and similar scripts. 
+
+Please note that ToolAnalysis remains the primary software framework for ANNIE. This repository is intended to host standalone helper scripts and utilities that complement the main codebase.
+
+## Repository Structure
+
+```text
+.
+├── cpp/
+├── docs/
+│   ├── script_catalog.md
+│   └── script_header_template.md
+├── python/
+├── .gitignore
+└── README.md
+```
+
+## Directory Description
+
+| Directory | Description                                             |
+| --------- | ------------------------------------------------------- |
+| `cpp/`    | C++ analysis and utility scripts                        |
+| `python/` | Python analysis and utility scripts                     |
+| `docs/`   | Script catalog and templates                            |
+
+
+## Repository Guidelines
+
+When adding new scripts to this repository:
+
+* Place scripts in the appropriate sub-directory (`cpp/` or `python/`).
+* The sub-directory name should reflect the primary purpose of the script(s) it contains.
+* All scripts must include the standard metadata header defined in `docs/script_header_template.md`.
+* Each script directory must contain a `README.md` describing the script, its inputs, outputs, dependencies (if applicable), and usage.
+* Add all new scripts to `docs/script_catalog.md`.
+* Update documentation whenever script functionality changes.
+* For c++ scripts, please include a Makefile to compile your application, unless it is to run as ROOT macro (though compiled scripts are preferred for compile-time error checking).
+* For python scripts, please specify your environment and all python modules, including versions which your script relies on.

cpp/offsetFit_MultipleLAPPD/README.md

@@ -0,0 +1,99 @@
+# offsetFit_MultipleLAPPD
+
+This script performs LAPPD timing offset fitting and takes `LAPPDTree.root` (produced by the `LAPPD_EB` toolchain) as input.
+
+## Requirements
+
+* All LAPPD events must appear in sequence.
+* All CTC events must appear in sequence.
+
+## Procedure
+
+1. Load `LAPPDTree.root`.
+2. Load the `TimeStamp` tree and obtain the run number and part file number.
+3. For each unique run number and part file number, perform the fit.
+4. For each LAPPD ID:
+
+   a. Loop over the `TimeStamp` tree and load:
+
+      * Data timestamp
+      * Data beamgate
+      * PPS for Board 0 and Board 1
+
+   b. Loop over the `Trig` (or `GTrig`) tree and load:
+
+      * CTC PPS (Trigger Word = 32)
+      * Target trigger word
+
+5. Find the number of resets in the LAPPD PPS stream:
+
+   * There must be at least one event in each reset.
+   * Based on the event index order, only fit before the reset that does not contain a data event.
+   * Save the data event and PPS index ordering.
+
+6. Use the target trigger word to perform the offset fit.
+7. Save the offset for:
+
+   * LAPPD ID
+   * Run Number
+   * Part File Number
+   * Event Index
+   * Reset Number
+
+8. Print information to output files.
+
+## Input Arguments
+
+The script takes five input arguments:
+
+| Argument               | Description                                                  |
+| ---------------------- | ------------------------------------------------------------ |
+| `filename`             | Input file (`LAPPDTree.root`)                                |
+| `fitTargetTriggerWord` | Undelayed Beam Trigger (14) for beam runs, 47 for laser runs |
+| `triggerGrouped`       | 1 for beam runs, 0 for laser runs                            |
+| `intervalInSeconds`    | See table below                                              |
+| `processPfNumber`      | 0                                                            |
+
+### intervalInSeconds
+
+| Run Range                | Value |
+| ------------------------ | ----- |
+| Run < 5140               | 10    |
+| Run = 6139 (Beam run)    | 10    |
+| Run ≥ 5140 (except 6139) | 5     |
+
+## Usage
+
+### Beam Runs
+
+#### Runs < 5140
+
+```bash
+root -l -q 'offsetFit_MultipleLAPPD.cpp("LAPPDTree.root", 14, 1, 10, 0)'
+```
+
+#### Runs ≥ 5140 (except Run 6139)
+
+```bash
+root -l -q 'offsetFit_MultipleLAPPD.cpp("LAPPDTree.root", 14, 1, 5, 0)'
+```
+
+#### Run 6139
+
+```bash
+root -l -q 'offsetFit_MultipleLAPPD.cpp("LAPPDTree.root", 14, 1, 10, 0)'
+```
+
+### Laser Runs
+
+#### Runs < 5140
+
+```bash
+root -l -q 'offsetFit_MultipleLAPPD.cpp("LAPPDTree.root", 47, 0, 10, 0)'
+```
+
+#### Runs ≥ 5140
+
+```bash
+root -l -q 'offsetFit_MultipleLAPPD.cpp("LAPPDTree.root", 47, 0, 5, 0)'
+```