Add improvements to package documentation

[azinneera]

Purpose

Improve the warning for Package.md deprecation.
Add generated module doc to BALA
Update Package.md validation in push command
Improve ProjectException error messages

Fixes #42825

Approach

Describe how you are implementing the solutions along with the design details.

Samples

Provide high-level details about the samples related to this feature.

Remarks

List any other known issues, related PRs, TODO items, or any other notes related to the PR.

Check List

• Read the Contributing Guide
• Updated Change Log
• Checked Tooling Support (#)
• Added necessary tests
  • Unit Tests
  • Spec Conformance Tests
  • Integration Tests
  • Ballerina By Example Tests
• Increased Test Coverage
• Added necessary documentation
  • API documentation
  • Module documentation in Module.md files
  • Ballerina By Examples

[codecov]

Codecov Report

Attention: Patch coverage is 64.28571% with 10 lines in your changes missing coverage. Please review.

Project coverage is 77.32%. Comparing base (b264541) to head (003ef5a).
Report is 49 commits behind head on master.

Files	Patch %	Lines
...rc/main/java/io/ballerina/projects/BalaWriter.java	61.53%	2 Missing and 3 partials ⚠️
...rc/main/java/io/ballerina/cli/cmd/PushCommand.java	71.42%	2 Missing ⚠️
.../java/io/ballerina/projects/util/ProjectPaths.java	33.33%	2 Missing ⚠️
...allerina/projects/directory/SingleFileProject.java	0.00%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff              @@
##             master   #43217      +/-   ##
============================================
- Coverage     77.36%   77.32%   -0.04%     
- Complexity    58454    58493      +39     
============================================
  Files          3454     3457       +3     
  Lines        219601   219817     +216     
  Branches      28871    28917      +46     
============================================
+ Hits         169898   169979      +81     
- Misses        40320    40442     +122     
- Partials       9383     9396      +13     

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