Document backend/bin scripts and utilities

.gitignore

@@ -1,2 +1,4 @@
 .DS_Store
 .env
+pr-summary.md
+backend/bin/sheets/

AGENTS.md

@@ -52,14 +52,32 @@
   - Accept a file path as the first positional argument and fall back to stdin.
   - Add an entry to `dotpy/README.md` following the existing format.
 
+## Pull Request Summaries
+
+- **When the developer asks for a PR summary**, write it to `pr-summary.md` in
+  the project root and open the file so they can select-all and copy from the
+  editor. `pr-summary.md` is listed in `.gitignore` and will never be
+  accidentally committed.
+- Use standard GitHub-flavoured Markdown: `##` / `###` headings, `**bold**`,
+  inline backticks, and bullet lists. Do not use HTML tags.
+- Structure the summary as:
+  1. **`## <Title>`** — one-line description matching the branch purpose.
+  2. **`### Summary`** — 2–4 sentences on what the PR does and why.
+  3. **`### Changes`** — one bold entry per changed file or directory with
+     bullet sub-points explaining what changed.
+  4. **`### Notes`** *(optional)* — follow-up items, known limitations, or
+     things the reviewer should verify manually.
+- Delete `pr-summary.md` after the PR is created; do not commit it.
+
 ## Markdown Formatting
 
 - **Format tables correctly**: Every column in a Markdown table must be padded so that all cells in that column (header, separator, and every data row) are the same width. The separator row must use dashes (`-`) at least as wide as the widest cell in each column. Mismatched widths cause IDE warnings ("Table is not correctly formatted").
   - Determine the widest cell in each column (considering the rendered source text, not the display text of links).
   - Pad every shorter cell with trailing spaces to match that width.
   - Use the same number of dashes in the separator row as the column width.
   - **The data rows — not just the header — define the required column width.** The header and separator must be padded/extended to match the widest data cell, not the other way around.
-  - To compute the exact separator, run: `python3 dotpy/calc_widths.py <file.md>` — it prints the maximum between-pipe width per column and the ready-to-paste separator row for every table in the file.
+  - To auto-format a table (strip whitespace, recalculate all widths, pad in place), run: `python3 dotpy/format_table.py <file.md>` — rewrites the file with every table correctly padded. **Use this first.**
+  - To compute the exact separator without editing, run: `python3 dotpy/calc_widths.py <file.md>` — it prints the maximum between-pipe width per column and the ready-to-paste separator row for every table in the file.
   - To validate alignment after editing, run: `python3 dotpy/check_tables.py <file.md>` — exits `0` if all tables are consistent, `1` with error details if not.
   - If a table requires very long lines (e.g., > 120 characters per row), prefer using a shorter link display text or a bullet-list format instead of a wide table.
 

DONE.md

@@ -1,5 +1,25 @@
 # DONE
 
+## 2026-04-22T00:00:00 — Backend Bin Scripts README
+Documented all 58 scripts and data files in `backend/bin/` (excluding
+`README.md` itself and the CSV inventory sheets under `sheets/`). Initial
+descriptions were synthesised from the v2 CSV inventory, then corrected via
+systematic file-by-file review. Thirteen factual errors were found and fixed;
+all corrections are documented as numbered footnotes in a "Review Notes"
+section appended to the README. All six Markdown tables pass `check_tables.py`
+validation.
+
+- [x] Extract descriptions for all files from inventory v2 CSV
+- [x] Document top-level scripts: `additonal_stats_data`, `consolidate_ips`, `embargo-item`, `find_crawlers`, `ip_stats_data`, `meta_file`, `meta_file_delete`, `meta_file_orcid`, `monthly_report`, `prep-logs`, `remove_ips`, `update_all_ip_table`
+- [x] Document `aptrust/` directory: `email-aptrust-bagging-errors`, `metadata2aptrust-info.xsl`, `metadata2bag-info.xsl`, `move-to-aptrust-regular`, `report-aptrust-status`, `saxon9he.jar`
+- [x] Document `cronjobs/` directory: `check-checksum`, `filter-media-cronjob`, `find-items-to-unrestrict-bio`, `find-items-to-unrestrict-rack`, `meta_file_author`, `meta_file_delete`, `meta_file_desc`, `perl_mailer`, `pubmedV2`, `report-about-dearborn-items`, `report-double-original`, `report-embargo`, `report-tombstone`, `report-too-many-authors`, `report-too-many-db-connections`, `update_author_list_too_long`
+- [x] Document `monthlies/` directory: `JOURNAL_SUBJECTS`, `change-type-martha`, `check-retiree.rb`, `clear-bit-description`, `find-authors-monthly`, `find-bit-change-perpmission`, `prepare-wiley`, `prepare-wiley_1`, `prepare-wiley_2`, `prepare-wiley_3`, `prepare-wiley_4`, `replace-funny-char-for-wiley`, `report-martha-types`, `report-users-out`, `update-orcid-values-monthly`
+- [x] Document `rackham/` directory: `prepare-rackham`, `report-for-rackham`
+- [x] Document `stats_monthlies/` directory: `StatsUtils.pm`, `find-alicia-stats`, `find-size-stats`, `monthly_admin_report`, `monthly_admin_report_for_bentley`, `monthly_individual_report`, `monthly_individual_report_based_on_author`
+- [x] Write `backend/bin/README.md` with all sections
+- [x] Validate README.md tables with `python3 dotpy/check_tables.py backend/bin/README.md`
+- [x] Verify with the developer that the task is complete
+
 ## 2026-04-21T00:00:00 — Address Minor Issues from PR Review (DEEPBLUE-466/Refactor)
 Resolved all actionable follow-up items flagged during the PR review: consolidated
 `dspace/backend.dockerfile` ant/wget layers, merged `dspace-uid/solr.dockerfile`

TODO.md

@@ -1,6 +1,7 @@
 # TODO
 
 
+
 ## Scrub Deleted `.cpt` Files from Git History
 The five encrypted config files (`backend/config/*.cpt`) and the production log
 (`backend/logs/dspace.log.2023-11-01`) were deleted from the working tree in