fix(gen2-migration): sandbox deployments fail in migration e2e due to missing dependencies

[iliapolo]

Description of changes

The migration tool no longer installs dependencies automatically during
gen2-migration generate. The e2e system now needs to run npm install
explicitly at each point where dependencies may have changed: after
generate, before ampx sandbox, and after checking out main for
refactor. Because npm install can modify the lock file, every branch
checkout is now preceded by a git add . && git commit to avoid
dirty-tree errors.

Other changes

Subprocess output: use stdio: 'inherit'

Subprocess calls (test scripts, ampx sandbox, configure.sh,
gen2-migration steps) were capturing stdout/stderr and selectively
re-logging interesting lines. This hid useful output during failures.
These calls now use stdio: 'inherit' so output streams directly to
the terminal. amplify push conditionally inherits only when the
logger is in debug mode (via a new Logger.isDebug() helper) since its esepecially noisy.

Remove interface-based DI layer

The interfaces/index.ts barrel defined interfaces (ILogger,
IFileManager, IAppSelector, etc.) that each had exactly one
implementation. Every class now references the concrete type directly.
The InitializeAppOptions interface moved to amplify-initializer.ts
where it belongs, and AWSCredentials/AWSProfileData moved to
aws-profile-manager.ts.

Simplify logger

Removed LogContext type and all context-passing from logger calls.
The logger now tracks the current app name via setAppName() and
includes it in every log line automatically, replacing the manual
{ appName, operation } threading.

Remove unused types

Deleted HostingConfiguration, DependencyConfiguration, and
LogContext from types/index.ts. Removed the hosting and
dependencies fields from AppConfiguration and
CategoryConfiguration. Updated the configuration-loader test
accordingly.

Move app validation earlier in CLI flow

App selection and validation now happens before environment detection
and credential resolution. This fails fast on a bad --app argument
before doing any expensive Atmosphere allocation work.

Tweak generateTimeBasedE2EAmplifyAppName

appName is now required (was optional). The function uses the first
10 characters as a prefix (was last 8) and drops seconds from the
timestamp to stay within the 20-char limit.

Shell script hardening and copy filter

Added set -euxo pipefail to configure.sh scripts. Added a copy
filter in DirectoryManager.copyDirectory to skip _snapshot and
node_modules directories when copying app sources.

Issue #, if available

N/A

Description of how you validated changes

• npx tsx src/cli.ts --app project-boards --profile default completes successfully.

Checklist

• PR description included
• yarn test passes
• Tests are changed or added
• Relevant documentation is changed or added (and PR referenced)
• New AWS SDK calls or CloudFormation actions have been added to relevant test and service IAM policies
• Pull request labels are added

By submitting this pull request, I confirm that my contribution is made under the terms of the Apache 2.0 license.