#16991: fix(config): add missing defaults to config snapshot path

## Summary - The `readConfigFileSnapshotInternal` function's file-exists path was missing `applyCompactionDefaults` and `applyContextPruningDefaults` in its defaults chain, while `loadConfig` and the no-file-exists path both correctly included them. This caused config snapshots read from existing files to lack compaction and context pruning defaults. - Added the two missing calls in the same nesting order as `loadConfig`, so all three paths now apply a consistent set of defaults. ## Test plan - Added `src/config/io.snapshot-defaults.test.ts` with two tests: - Verifies `compaction.mode` is set to `"safeguard"` when a config file exists with `agents.defaults` - Verifies the same default is applied when no config file exists (existing behavior, regression guard) - Existing `io.write-config.test.ts` tests continue to pass <!-- greptile_comment --> <h3>Greptile Summary</h3> This PR fixes an inconsistency in the config defaults chain within `readConfigFileSnapshotInternal` in `src/config/io.ts`. The file-exists path was missing calls to `applyCompactionDefaults` and `applyContextPruningDefaults`, while both `loadConfig` and the no-file-exists path correctly included them. This caused config snapshots read from existing files to lack compaction and context pruning defaults (e.g., `compaction.mode` not being set to `"safeguard"`). - Adds `applyCompactionDefaults(applyContextPruningDefaults(...))` wrapping in the file-exists path of `readConfigFileSnapshotInternal`, matching the same nesting order as `loadConfig` (lines 582-590) - Adds a new test file `io.snapshot-defaults.test.ts` with two focused tests covering both the file-exists and no-file-exists paths - The fix is minimal, correctly ordered, and well-tested <h3>Confidence Score: 5/5</h3> - This PR is safe to merge — it adds two missing function calls to align a defaults chain with existing correct patterns. - The change is a straightforward, low-risk bug fix that adds two missing defaults function calls (`applyCompactionDefaults`, `applyContextPruningDefaults`) to match the already-correct patterns in `loadConfig` and the no-file-exists path. The nesting order is verified to be consistent across all three paths. New tests cover the exact scenario. No behavioral regressions are expected. - No files require special attention. _{Last reviewed commit: 20b65ad} <!-- greptile_other_comments_section --> <!-- /greptile_comment -->