Fix two issues regarding the PD Code of the Link class

[soehms]

1. Currently, the _directions_of_edges method returns incorrect results if a link's pd_code contains loops. Example:

sage: K = Link([[1, 5, 12, 6], [6, 12, 7, 11], [9, 10, 10, 11], [8, 1, 9, 4], [7, 5, 8, 4]])
sage: K._directions_of_edges()
({12: [1, 5, 12, 6], 11: [6, 12, 7, 11], 10: [9, 10, 10, 11], 7: [6, 12, 7, 11], 8: [7, 5, 8, 4], 9: [8, 1, 9, 4], 1: [1, 5, 12, 6], 4: [8, 1, 9, 4], 5: [7, 5, 8, 4], 6: [1, 5, 12, 6]},
 {12: [6, 12, 7, 11], 11: [9, 10, 10, 11], 10: [9, 10, 10, 11], 7: [7, 5, 8, 4], 8: [8, 1, 9, 4], 9: [9, 10, 10, 11], 1: [8, 1, 9, 4], 4: [7, 5, 8, 4], 5: [1, 5, 12, 6], 6: [6, 12, 7, 11]})

Here, the crossing involving the loop [9, 10, 10, 11] appears three times as a head and only once as a tail. The implementation calculates the position of an edge within the crossing using index; however, this function never returns the second position of the 10 within the crossing.

2. The PD-Code generated from the braid and DT notations does not strictly adhere to standard conventions (such as those explained at KnotInfo).

This poses a problem when these PD-Codes are used as input for other programs (such as Khoca) that implicitly assume that consecutive segments of a component are labeled with consecutive numbers.

The following is implemented

1. A new public method components, which explicitly returns the components of a link as lists of edge labels derived from the PD code.
2. This method is used for a new implementation of _directions_of_edges which fixes the first issue, in number_of_components as well as in two new internal methods (_is_pd_normalized and _normalize_pd), which assist in calculating a normalized PD code of a link given in braid or DT notation.
3. A warning is added in __init__ to alert the user to non-normalized PD inputs.

📝 Checklist

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