feat: adding all missing file references

[cka-y]

Summary:

This pull request refactors and reorganizes several GTFS validator notices, moving deprecated and internal notices to new locations, and updates notice metadata to improve clarity and maintainability. It also enhances the annotation of validation notices with explicit references to the relevant GTFS files.

Please make sure these boxes are checked before submitting your pull request - thanks!

• Run the unit tests with gradle test to make sure you didn't break anything
• Add or update any needed documentation to the repo
• Format the title like "feat: [new feature short description]". Title must follow the Conventional Commit Specification(https://www.conventionalcommits.org/en/v1.0.0/).
• Linked all relevant issues
• Include screenshot(s) showing how this pull request works and fixes the issue(s)

[github-actions]

📝 Acceptance Test Report

📋 Summary

✅ The rule acceptance has passed for commit 1e003fe
Download the full acceptance test report here (report will disappear after 90 days).

📊 Notices Comparison

New Errors (0 out of 987 datasets, ~0%) ✅

No changes were detected due to the code change.

Dropped Errors (0 out of 987 datasets, ~0%) ✅

No changes were detected due to the code change.

New Warnings (0 out of 987 datasets, ~0%) ✅

No changes were detected due to the code change.

Dropped Warnings (0 out of 987 datasets, ~0%) ✅

No changes were detected due to the code change.

🛡️ Corruption Check

16 out of 1003 sources (~2 %) are corrupted.

Dataset	Ref Report Exists	Ref Report Readable	Latest Report Exists	Latest Report Readable
mdb-1114	✅	✅	✅	✅
mdb-1123	✅	✅	✅	✅
mdb-1332	✅	✅	✅	✅
mdb-1808	✅	✅	✅	✅
mdb-1953	✅	✅	✅	✅
mdb-227	✅	✅	✅	✅
mdb-383	✅	✅	✅	✅
mdb-55	✅	✅	✅	✅
mdb-606	✅	✅	✅	✅
mdb-609	✅	✅	✅	✅
mdb-655	✅	✅	✅	✅
mdb-780	✅	✅	✅	✅
mdb-789	✅	✅	✅	✅
mdb-806	✅	✅	✅	✅
mdb-9	✅	✅	✅	✅
mdb-907	✅	✅	✅	✅

⏱️ Performance Assessment

📈 Validation Time

Assess the performance in terms of seconds taken for the validation process.

Time Metric	Dataset ID	Reference (s)	Latest (s)	Difference (s)
Average	--	5.50	5.61	⬆️+0.11
Median	--	1.55	1.66	⬆️+0.11
Standard Deviation	--	22.23	22.92	⬆️+0.69
Minimum in References Reports	mdb-1819	0.44	0.82	⬆️+0.38
Maximum in Reference Reports	mdb-2014	601.25	625.94	⬆️+24.69
Minimum in Latest Reports	mdb-1788	0.48	0.47	⬇️-0.01
Maximum in Latest Reports	mdb-2014	601.25	625.94	⬆️+24.69

📜 Memory Consumption

Metric	Dataset ID	Reference (s)	Latest (s)	Difference (s)
Average	--	557.87 MiB	561.82 MiB	⬆️+3.95 MiB
Median	--	327.93 MiB	327.93 MiB	⬇️0 bytes
Standard Deviation	--	949.58 MiB	960.31 MiB	⬆️+10.73 MiB
Minimum in References Reports	mdb-61	40.02 MiB	415.93 MiB	⬆️+375.91 MiB
Maximum in Reference Reports	mdb-2014	9.08 GiB	9.11 GiB	⬆️+25.58 MiB
Minimum in Latest Reports	mdb-2329	55.71 MiB	41.90 MiB	⬇️-13.81 MiB
Maximum in Latest Reports	mdb-2014	9.08 GiB	9.11 GiB	⬆️+25.58 MiB

[davidgamez]

LGTM!