Make repeated IPA and Mac app builds incremental (#279)

Reuse unchanged IPA entries through the packing index and APFS clones,
and keep Mac app and derived-profile shader outputs while their inputs
match. Preserve main's shader regression checks and .NET discovery.

Count uncompressed bytes in streamed files so a size change aborts the
pack without replacing the previous IPA or index. Cover both deflated
and stored streams with growth and shrinkage regression tests, and
record the cause and fix in the packing reference.

Co-authored-by: Suraj Mandal <surajmandalcell@gmail.com>
(cherry picked from commit 09f3778c36)

docs/reference/packing.md

@@ -9,6 +9,15 @@
 - **Fix:** `scripts/build_ipa_from_nsp.py` `configure_dotnet` derives the root from the `Microsoft.NETCore.App` entry in `dotnet --list-runtimes`, using the build's environment, before any extraction or survey. It exports `DOTNET_ROOT` both to that environment and to `os.environ`, for tools launched with an explicit environment and those that inherit it. Caller-supplied roots, including architecture-specific overrides, retain precedence. A failed or malformed probe leaves the environment unchanged rather than guessing the wrapper's directory.
 - **Found on:** [Balatro](../../dm/games/0100CD801CE5E000/README.md), first extraction with Homebrew .NET ([PR #284](https://github.com/seedds/nxnative/pull/284)). Applies to every game's build on that installation setup.
 
+## IPA archives
+
+### A streamed file changes size and the IPA fails its CRC check
+
+- **Symptom:** packing succeeds, but `unzip -t` or Python's `ZipFile.testzip()` reports a bad CRC for a large deflated file.
+- **Cause:** `pack_ipa.py` wrote the uncompressed size collected before reading. Its streaming check compared the output size only for stored files, so a compressible file that grew or shrank still published an archive with the old size.
+- **Fix:** count uncompressed bytes as they are read and compare them with the listed size before completing either streamed method. A mismatch stops the pack and removes the partial archive, preserving the previous IPA and its reuse index. Regression tests cover growth and shrinkage with both deflate and store.
+- **Found on:** synthetic IPA inputs while reviewing [PR #279](https://github.com/seedds/nxnative/pull/279); no game files required.
+
 ## Compressed inputs
 
 ### NSZ decompression rejects `--keys`