Update documentation about encoding 'sex'

[monicacecilia]

There is a discrepancy between some PED-related bioinformatics conventions and the architecture of the Phenopackets schema.

1. PEDFILE / PLINK Standard: In standard genetics workflows (like .ped files or PLINK), sex is conventionally encoded using specific integers:

• 1 = Male (easy to remember: 1 X chromosome)
• 2 = Female (2 X chromosomes)

2. Phenopackets Protobuf Definition: The Phenopackets schema assigned the internal enum integers differently:

• FEMALE = 1
• MALE = 2

We need to update the documentation to clarify things:

• This discrepancy doesn't actually break anything functionally. When users create a Phenopacket in JSON or YAML, they don't type 1 or 2. They use the string literals "FEMALE" or "MALE".
• The Protobuf parser handles mapping the string to the internal integer behind the scenes. However, as seen in Issue Is "Sex" correctly labelled in the Pedigree example and Sex documentation  #391, when developers look at the raw .proto files or the auto-generated documentation, they see FEMALE=1 and MALE=2. Because they are used to the PEDFILE standard, they immediately flag this as a "bug" or assume it will cause massive data miscoding.
• We don't need to actually change the Protobuf integers (which would be a breaking change to the schema's binary serialization), but we do need to add clear documentation so users stop getting confused.

fixes #321

[monicacecilia]

To update the code comments and the public-facing documentation:

1. Update the .proto file comments: In the .proto file where the Sex enum is defined, add a comment directly above the enum. It will automatically carry over into auto-generated docs. For example, we could update to:

// Note: The integer values used in this enum are internal Protocol Buffer indices.
// They DO NOT correspond to standard PED/PLINK file integer encodings (where Male=1, Female=2).
// When generating JSON/YAML Phenopackets, always use the string representation
// (e.g., "MALE", "FEMALE") rather than these integer values.
enum Sex {
UNKNOWN_SEX = 0;
FEMALE = 1;
MALE = 2;
OTHER_SEX = 3;
}

2. Update the ReadTheDocs: In docs/sex.rst and docs/pedigree.rst, add a prominent warning. Something along the lines of:

• Note on Pedigree / PED format compatibility: In standard genetic pedigree files (like PLINK), sex is typically encoded as 1 for Male and 2 for Female. You may notice that the Phenopackets internal schema assigns the integer 1 to FEMALE and 2 to MALE. Do not use integers to encode sex in Phenopackets. This discrepancy will not affect your data because Phenopackets JSON and YAML implementations require you to use the explicit string values ("MALE", "FEMALE", "UNKNOWN_SEX"). The underlying software will automatically handle the correct data serialization.

fixes #391