feat/v2-deprecations: Warn on legacy config knobs and flip docs to v2

[vedanthvdev]

Summary

Phase 2 of the v2 rollout per docs/DESIGN-v2.md §4 — signal that v1 config is on its way out without breaking any existing build.

Three things:

1. Per-run deprecation warnings for callers who explicitly set runAllIfNoMatches, runAllOnNonJavaChange, or excludePaths. Zero-config installs stay silent.
2. README examples flipped to v2. Legacy knobs removed from the main config sample and the AffectedTestsExtension javadoc. Behaviour-reference table drops the legacy-flag mentions from its "override knob" column.
3. README Migration section expanded with a deprecation timeline, before/after table, worked example, and a per-knob decision tree.

What the warnings look like

WARNING: [affected-tests] 'runAllIfNoMatches' is deprecated and will be removed in v2.0.0.
  Replace it with per-situation actions (onEmptyDiff / onAllFilesIgnored /
  onAllFilesOutOfScope / onDiscoveryEmpty), each set to 'full_suite' to match
  runAllIfNoMatches=true, or 'skipped' to match runAllIfNoMatches=false.
  See README.md section 'Migrating from v1 config'.

WARNING: [affected-tests] 'runAllOnNonJavaChange' is deprecated and will be removed in v2.0.0.
  Replace it with 'onUnmappedFile' (full_suite / selected / skipped).
  See README.md section 'Migrating from v1 config'.

WARNING: [affected-tests] 'excludePaths' is deprecated and will be removed in v2.0.0.
  Rename it to 'ignorePaths' — identical semantics, and leaving it unset picks up
  the broader v2 default list (markdown, generated/, licence/changelog, images).
  See README.md section 'Migrating from v1 config'.

Emitted via `Logger.warn(...)` on every `affectedTest` run, immediately before the summary line so the warning sits adjacent to the config it describes. Gradle's deprecation dashboard and build-scan `warnings` stream pick this up as a first-class warning (not an info line).

Why the detection is on *caller intent*, not resolution path

The config builder uses `Boolean` / `List` nullable backing fields for the legacy setters. `deprecationWarnings()` is populated by inspecting those nullables directly — `null` means "caller never typed it", non-null means "caller typed it".

This matters: zero-config installs still internally route through the legacy-boolean shim (because the effective `onEmptyDiff` default etc. is derived from the `runAllIfNoMatches=false` hardcoded fallback). If the detection were based on the shim walking that path, we'd spam a warning on every zero-config build and train users to ignore deprecations before the real ones land. Instead, only callers who actually typed the old name in their `build.gradle` see anything.

Migration guide highlights

The new README section boils down to one insight: for 95% of legacy configs, a single `mode = "ci"` line replaces both booleans. The decision tree covers the remaining 5% (specifically: `runAllIfNoMatches=false` → just delete it; `runAllOnNonJavaChange=false` → `onUnmappedFile = "selected"`).

Before:
```groovy
affectedTests {
runAllIfNoMatches = true
runAllOnNonJavaChange = true
excludePaths = ["/generated/"]
transitiveDepth = 4
}
```

After:
```groovy
affectedTests {
mode = "ci"
}
```

(v2's `ignorePaths` default already covers `/generated/`, and `transitiveDepth = 4` is the new default.)

Tests

• `AffectedTestsConfigTest` gains 7 new tests locking down:
  • Zero warnings for zero-config builds (the key back-compat guarantee).
  • One warning per legacy knob, each containing the knob name and the v2 replacement name in its text.
  • Stable ordering (runAllIfNoMatches → runAllOnNonJavaChange → excludePaths) when multiple are set, so CI log greps stay deterministic.
  • The warnings list is unmodifiable — prevents the Gradle task from accidentally mutating a shared config.
  • v2-native configs (mode, onXxx, ignorePaths, outOfScope\*) emit zero warnings, so migrators have a clear target.

Deprecation timeline

Release	Behaviour
v1.9.x and earlier	Legacy knobs work silently.
v1.10.x (this PR)	Legacy knobs still work. Per-run `WARNING` names each one and its replacement. Zero-config users see nothing.
v2.0.0 (next major)	Legacy knobs removed. Gradle will fail configuration if any of them appear in `build.gradle`.

Test plan

• `./gradlew check` (core + gradle unit + functionalTest + validatePlugins) passes locally.
• CI run on this branch stays green.
• Verify on the existing Modulr security-service MR that switching to `mode = "ci"` + removing the legacy flags produces the same effective behaviour.